diff --git a/404.html b/404.html
index 23cc217..6a39730 100644
--- a/404.html
+++ b/404.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="https://rmgpanw.github.io/gtexr/index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index a35cbde..e25f194 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 9f940c9..8ecd719 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/developer_guide.html b/articles/developer_guide.html
index 1b7f1e5..b392ce4 100644
--- a/articles/developer_guide.html
+++ b/articles/developer_guide.html
@@ -26,7 +26,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/gtexr.html b/articles/gtexr.html
index 0d70df7..6d30d22 100644
--- a/articles/gtexr.html
+++ b/articles/gtexr.html
@@ -26,7 +26,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index e73567a..069373e 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 355aaeb..8421f91 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -66,14 +66,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Warwick A, Zuckerman B, Olvera-Barrios A, Ung C, Luben R (2024).
 <em>gtexr: Query the GTEx Portal API</em>.
-R package version 0.0.0.9000,
+R package version 0.1.0,
 https://github.com/rmgpanw/gtexr, <a href="https://rmgpanw.github.io/gtexr/">https://rmgpanw.github.io/gtexr/</a>.
 </p>
       <pre>@Manual{,
   title = {gtexr: Query the GTEx Portal API},
   author = {Alasdair Warwick and Benjamin Zuckerman and Abraham Olvera-Barrios and Chuin Ying Ung and Robert Luben},
   year = {2024},
-  note = {R package version 0.0.0.9000,
+  note = {R package version 0.1.0,
     https://github.com/rmgpanw/gtexr},
   url = {https://rmgpanw.github.io/gtexr/},
 }</pre>
diff --git a/index.html b/index.html
index ef8bec9..517ce7d 100644
--- a/index.html
+++ b/index.html
@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -152,6 +152,7 @@ <h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"
   </main><aside class="col-md-3"><div class="links">
 <h2 data-toc-skip>Links</h2>
 <ul class="list-unstyled">
+<li><a href="https://cloud.r-project.org/package=gtexr" class="external-link">View on CRAN</a></li>
 <li><a href="https://github.com/rmgpanw/gtexr/" class="external-link">Browse source code</a></li>
 <li><a href="https://github.com/rmgpanw/gtexr/issues" class="external-link">Report a bug</a></li>
 </ul>
diff --git a/news/index.html b/news/index.html
index c9a039e..d446410 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,7 +37,7 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="development version" id="gtexr-development-version">gtexr (development version)<a class="anchor" aria-label="anchor" href="#gtexr-development-version"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.1.0" id="gtexr-010">gtexr 0.1.0<a class="anchor" aria-label="anchor" href="#gtexr-010"></a></h2><p class="text-muted">CRAN release: 2024-09-19</p>
 <ul><li>Initial CRAN submission.</li>
 </ul></div>
   </main></div>
diff --git a/pkgdown.yml b/pkgdown.yml
index dafe436..050e8c2 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   developer_guide: developer_guide.html
   gtexr: gtexr.html
-last_built: 2024-09-18T23:57Z
+last_built: 2024-09-19T21:27Z
 urls:
   reference: https://rmgpanw.github.io/gtexr/reference
   article: https://rmgpanw.github.io/gtexr/articles
diff --git a/reference/calculate_expression_quantitative_trait_loci.html b/reference/calculate_expression_quantitative_trait_loci.html
index fb176c8..656bcdc 100644
--- a/reference/calculate_expression_quantitative_trait_loci.html
+++ b/reference/calculate_expression_quantitative_trait_loci.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -132,16 +132,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 670 × 15</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      data error gencodeId         geneSymbol genotypes hetCount homoAltCount</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span>  1.86  0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> -<span style="color: #BB0000;">1.06</span>  0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> -<span style="color: #BB0000;">0.618</span> 0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> -<span style="color: #BB0000;">1.39</span>  0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span>  0.329 0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span>  1.37  0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span>  0.832 0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span>  0.118 0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span>  0.197 0.148 ENSG00000203782.5 LOR                0       38            0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> -<span style="color: #BB0000;">0.442</span> 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span>  0.949 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span>  1.86  0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> -<span style="color: #BB0000;">0.641</span> 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span>  0.683 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> -<span style="color: #BB0000;">0.321</span> 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span>  0.539 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span>  0.266 0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> -<span style="color: #BB0000;">1.10</span>  0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> -<span style="color: #BB0000;">1.88</span>  0.148 ENSG00000203782.5 LOR                0       38            0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> -<span style="color: #BB0000;">1.03</span>  0.148 ENSG00000203782.5 LOR                0       38            0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 660 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 8 more variables: homoRefCount &lt;int&gt;, maf &lt;dbl&gt;, nes &lt;dbl&gt;, pValue &lt;dbl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   pValueThreshold &lt;dbl&gt;, tStatistic &lt;dbl&gt;, tissueSiteDetailId &lt;chr&gt;,</span></span>
diff --git a/reference/calculate_ieqtls.html b/reference/calculate_ieqtls.html
index cda5b3a..34dcf34 100644
--- a/reference/calculate_ieqtls.html
+++ b/reference/calculate_ieqtls.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculate_isqtls.html b/reference/calculate_isqtls.html
index f74d443..7fb87d4 100644
--- a/reference/calculate_isqtls.html
+++ b/reference/calculate_isqtls.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculate_splicing_quantitative_trait_loci.html b/reference/calculate_splicing_quantitative_trait_loci.html
index a5d1df9..8c9df7c 100644
--- a/reference/calculate_splicing_quantitative_trait_loci.html
+++ b/reference/calculate_splicing_quantitative_trait_loci.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/download.html b/reference/download.html
index 57aac88..476fa2f 100644
--- a/reference/download.html
+++ b/reference/download.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_annotation.html b/reference/get_annotation.html
index e07b2bf..a05e394 100644
--- a/reference/get_annotation.html
+++ b/reference/get_annotation.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_clustered_median_exon_expression.html b/reference/get_clustered_median_exon_expression.html
index 6b854b3..072583c 100644
--- a/reference/get_clustered_median_exon_expression.html
+++ b/reference/get_clustered_median_exon_expression.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_clustered_median_gene_expression.html b/reference/get_clustered_median_gene_expression.html
index 4167b13..08caff6 100644
--- a/reference/get_clustered_median_gene_expression.html
+++ b/reference/get_clustered_median_gene_expression.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_clustered_median_junction_expression.html b/reference/get_clustered_median_junction_expression.html
index a68afc0..b583c26 100644
--- a/reference/get_clustered_median_junction_expression.html
+++ b/reference/get_clustered_median_junction_expression.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_clustered_median_transcript_expression.html b/reference/get_clustered_median_transcript_expression.html
index fc3a9c7..00bd5ab 100644
--- a/reference/get_clustered_median_transcript_expression.html
+++ b/reference/get_clustered_median_transcript_expression.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_collapsed_gene_model_exon.html b/reference/get_collapsed_gene_model_exon.html
index b073161..e84fe53 100644
--- a/reference/get_collapsed_gene_model_exon.html
+++ b/reference/get_collapsed_gene_model_exon.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_dataset_info.html b/reference/get_dataset_info.html
index 9ef5eba..b6157a4 100644
--- a/reference/get_dataset_info.html
+++ b/reference/get_dataset_info.html
@@ -7,7 +7,7 @@
 
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index 5e0329f..d172384 100644
--- a/reference/get_significant_single_tissue_ieqtls.html
+++ b/reference/get_significant_single_tissue_ieqtls.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_significant_single_tissue_isqtls.html b/reference/get_significant_single_tissue_isqtls.html
index 0e32659..0168634 100644
--- a/reference/get_significant_single_tissue_isqtls.html
+++ b/reference/get_significant_single_tissue_isqtls.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_significant_single_tissue_sqtls.html b/reference/get_significant_single_tissue_sqtls.html
index e9dc942..5d70f55 100644
--- a/reference/get_significant_single_tissue_sqtls.html
+++ b/reference/get_significant_single_tissue_sqtls.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_single_nucleus_gex.html b/reference/get_single_nucleus_gex.html
index f903e29..f07c8d8 100644
--- a/reference/get_single_nucleus_gex.html
+++ b/reference/get_single_nucleus_gex.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_single_nucleus_gex_summary.html b/reference/get_single_nucleus_gex_summary.html
index 5739bab..a8b43d4 100644
--- a/reference/get_single_nucleus_gex_summary.html
+++ b/reference/get_single_nucleus_gex_summary.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_sqtl_genes.html b/reference/get_sqtl_genes.html
index 2e30c3d..33a39cb 100644
--- a/reference/get_sqtl_genes.html
+++ b/reference/get_sqtl_genes.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_subject.html b/reference/get_subject.html
index 35425fd..10d7f7a 100644
--- a/reference/get_subject.html
+++ b/reference/get_subject.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_tissue_site_detail.html b/reference/get_tissue_site_detail.html
index 5e83343..cd1778e 100644
--- a/reference/get_tissue_site_detail.html
+++ b/reference/get_tissue_site_detail.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_top_expressed_genes.html b/reference/get_top_expressed_genes.html
index f281d43..39fdd2c 100644
--- a/reference/get_top_expressed_genes.html
+++ b/reference/get_top_expressed_genes.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_transcripts.html b/reference/get_transcripts.html
index 45bd88b..337979e 100644
--- a/reference/get_transcripts.html
+++ b/reference/get_transcripts.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_variant.html b/reference/get_variant.html
index 7ee2a46..330d087 100644
--- a/reference/get_variant.html
+++ b/reference/get_variant.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_variant_by_location.html b/reference/get_variant_by_location.html
index 9079ec0..cad1dea 100644
--- a/reference/get_variant_by_location.html
+++ b/reference/get_variant_by_location.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/gtexr-package.html b/reference/gtexr-package.html
index 5b0ffd3..52b2945 100644
--- a/reference/gtexr-package.html
+++ b/reference/gtexr-package.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/gtexr_arguments.html b/reference/gtexr_arguments.html
index 7144327..96ec610 100644
--- a/reference/gtexr_arguments.html
+++ b/reference/gtexr_arguments.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index c115b6e..443c4a6 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">gtexr</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index c99695b..e22bbe0 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://rmgpanw.github.io/gtexr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 gtexr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/developer_guide.html","id":"functions","dir":"Articles","previous_headings":"","what":"Functions","title":"Developer guide","text":"Function name title API endpoint lower case, words separated underscores. @description section copied verbatim API documentation site ends link corresponding API endpoint documentation. notes may added @details. Names match API endpoint, except argument accepts array (vector R) values, case pluralised.1 Default values also match API endpoint. Query parameters flagged “required” GTEx Portal API documentation default values.2 documented gtexr_arguments.R. functions therefore use @inheritParams gtexr_arguments documentation. Use @family roxygen tag match categories API documentation. used categorise functions pkgdown site reference page. Return tibble. first example @examples must produce output single function call without assignment (e.g. get_news_items(), x <- get_news_items()). used pre-populate argument values gtexr shiny app working example. examples surrounded \\dontrun{}.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"shiny-app","dir":"Articles","previous_headings":"","what":"Shiny app","title":"Introduction to gtexr","text":"Users can try functions interatively ⭐gtexr shiny app⭐, pre-populates query parameters first working example function’s documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"Introduction to gtexr","text":"rest vignette outlines example applications gtexr.","code":"library(gtexr) library(dplyr) library(purrr)"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-build-37-coordinates-for-a-variant","dir":"Articles","previous_headings":"Examples","what":"Get build 37 coordinates for a variant","title":"Introduction to gtexr","text":"","code":"get_variant(snpId = \"rs1410858\") |>   tidyr::separate(     col = b37VariantId,     into = c(       \"chromosome\",       \"position\",       \"reference_allele\",       \"alternative_allele\",       \"genome_build\"     ),     sep = \"_\",     remove = FALSE   ) |>   select(snpId:genome_build) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #>   snpId     b37VariantId chromosome position reference_allele alternative_allele #>   <chr>     <chr>        <chr>      <chr>    <chr>            <chr>              #> 1 rs1410858 1_153182116… 1          1531821… C                A                  #> # ℹ 1 more variable: genome_build <chr>"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-gene-symbol-to-versioned-gencode-id","dir":"Articles","previous_headings":"Examples","what":"Convert gene symbol to versioned GENCODE ID","title":"Introduction to gtexr","text":"Use get_gene() get_genes()","code":"get_genes(\"CRP\") |>   select(geneSymbol, gencodeId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #>   geneSymbol gencodeId          #>   <chr>      <chr>              #> 1 CRP        ENSG00000132693.12"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-rsid-to-gtex-variant-id","dir":"Articles","previous_headings":"Examples","what":"Convert rsID to GTEx variant ID","title":"Introduction to gtexr","text":"Use get_variant()","code":"get_variant(snpId = \"rs1410858\") |>   select(snpId, variantId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #>   snpId     variantId              #>   <chr>     <chr>                  #> 1 rs1410858 chr1_153209640_C_A_b38"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"for-a-gene-of-interest-which-tissues-have-significant-cis-eqtls","dir":"Articles","previous_headings":"Examples","what":"For a gene of interest, which tissues have significant cis-eQTLs?","title":"Introduction to gtexr","text":"Use get_significant_single_tissue_eqtls() (note requires versioned GENCODE IDs)","code":"gene_symbol_of_interest <- \"CRP\"  gene_gencodeId_of_interest <- get_genes(gene_symbol_of_interest) |>   pull(gencodeId) |>   suppressMessages()  gene_gencodeId_of_interest |>   get_significant_single_tissue_eqtls() |>   distinct(geneSymbol, gencodeId, tissueSiteDetailId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 93 #> # A tibble: 3 × 3 #>   geneSymbol gencodeId          tissueSiteDetailId                  #>   <chr>      <chr>              <chr>                               #> 1 CRP        ENSG00000132693.12 Thyroid                             #> 2 CRP        ENSG00000132693.12 Esophagus_Gastroesophageal_Junction #> 3 CRP        ENSG00000132693.12 Muscle_Skeletal"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-data-for-non-eqtl-variants","dir":"Articles","previous_headings":"Examples","what":"Get data for non-eQTL variants","title":"Introduction to gtexr","text":"analyses (e.g. Mendelian randomisation) require data variants may may significant eQTLs. Use calculate_expression_quantitative_trait_loci() purrr::map() retrieve data multiple variants","code":"variants_of_interest <- c(\"rs12119111\", \"rs6605071\", \"rs1053870\")  variants_of_interest |>   set_names() |>   map(     \\(x) calculate_expression_quantitative_trait_loci(       tissueSiteDetailId = \"Liver\",       gencodeId = \"ENSG00000237973.1\",       variantId = x     )   ) |>   bind_rows(.id = \"rsid\") |>      # optionally, reformat output - first extract genomic coordinates and alleles   tidyr::separate(     col = \"variantId\",     into = c(       \"chromosome\",       \"position\",       \"reference_allele\",       \"alternative_allele\",       \"genome_build\"     ),     sep = \"_\"   ) |>      # ...then ascertain alternative_allele frequency   mutate(     alt_allele_count = (2 * homoAltCount) + hetCount,     total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),     alternative_allele_frequency = alt_allele_count / total_allele_count   ) |>      select(     rsid,     beta = nes,     se = error,     pValue,     minor_allele_frequency = maf,     alternative_allele_frequency,     chromosome:genome_build,     tissueSiteDetailId   ) #> # A tibble: 3 × 12 #>   rsid         beta     se  pValue minor_allele_frequency alternative_allele_f…¹ #>   <chr>       <dbl>  <dbl>   <dbl>                  <dbl>                  <dbl> #> 1 rs121191…  0.0270 0.0670 6.88e-1                 0.365                   0.635 #> 2 rs6605071 -0.601  0.166  3.88e-4                 0.0409                  0.959 #> 3 rs1053870  0.0247 0.0738 7.38e-1                 0.214                   0.214 #> # ℹ abbreviated name: ¹​alternative_allele_frequency #> # ℹ 6 more variables: chromosome <chr>, position <chr>, reference_allele <chr>, #> #   alternative_allele <chr>, genome_build <chr>, tissueSiteDetailId <chr>"},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alasdair Warwick. Author, maintainer, copyright holder. Benjamin Zuckerman. Author. Abraham Olvera-Barrios. Author. Chuin Ying Ung. Author. Robert Luben. Author.","code":""},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Warwick , Zuckerman B, Olvera-Barrios , Ung C, Luben R (2024). gtexr: Query GTEx Portal API. R package version 0.0.0.9000, https://github.com/rmgpanw/gtexr, https://rmgpanw.github.io/gtexr/.","code":"@Manual{,   title = {gtexr: Query the GTEx Portal API},   author = {Alasdair Warwick and Benjamin Zuckerman and Abraham Olvera-Barrios and Chuin Ying Ung and Robert Luben},   year = {2024},   note = {R package version 0.0.0.9000,     https://github.com/rmgpanw/gtexr},   url = {https://rmgpanw.github.io/gtexr/}, }"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"gtexr-","dir":"","previous_headings":"","what":"Query the GTEx Portal API","title":"Query the GTEx Portal API","text":"goal gtexr provide convenient R interface GTEx Portal API V2. New R? Try ⭐shiny app⭐.","code":""},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Query the GTEx Portal API","text":"can install package CRAN: can install development version gtexr GitHub :","code":"install.packages(\"gtexr\") # install.packages(\"devtools\") devtools::install_github(\"rmgpanw/gtexr\")"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Query the GTEx Portal API","text":"Get general information GTEx service: Retrieve eQTL genes whole blood tissue: Retrieve significant eQTLs one genes:","code":"library(gtexr) get_service_info() #> # A tibble: 1 × 9 #>   id     name  version organization_name organization_url description contactUrl #>   <chr>  <chr> <chr>   <chr>             <chr>            <chr>       <chr>      #> 1 org.g… GTEx… 2.0.0   GTEx Project      https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl <chr>, environment <chr> get_eqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (12360) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 50 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 12360 #> # A tibble: 250 × 10 #>    tissueSiteDetailId ontologyId  datasetId empiricalPValue gencodeId geneSymbol #>    <chr>              <chr>       <chr>               <dbl> <chr>     <chr>      #>  1 Whole_Blood        UBERON:001… gtex_v8          1.05e- 9 ENSG0000… WASH7P     #>  2 Whole_Blood        UBERON:001… gtex_v8          1.06e-25 ENSG0000… RP11-34P1… #>  3 Whole_Blood        UBERON:001… gtex_v8          6.31e- 2 ENSG0000… CICP27     #>  4 Whole_Blood        UBERON:001… gtex_v8          8.71e- 9 ENSG0000… RP11-34P1… #>  5 Whole_Blood        UBERON:001… gtex_v8          6.01e-20 ENSG0000… RP11-34P1… #>  6 Whole_Blood        UBERON:001… gtex_v8          6.96e- 9 ENSG0000… RP11-34P1… #>  7 Whole_Blood        UBERON:001… gtex_v8          3.10e- 4 ENSG0000… RP11-34P1… #>  8 Whole_Blood        UBERON:001… gtex_v8          1.92e- 3 ENSG0000… ABC7-4304… #>  9 Whole_Blood        UBERON:001… gtex_v8          1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood        UBERON:001… gtex_v8          7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, qValue <dbl> get_significant_single_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs12128960 159343657 RS12128960 chr1_1593… CRP        8.52e-5 CRP             #>  2 rs12132451 159344052 RS12132451 chr1_1593… CRP        7.92e-5 CRP             #>  3 rs12136402 159347493 RS12136402 chr1_1593… CRP        7.92e-5 CRP             #>  4 rs10908709 159350390 RS10908709 chr1_1593… CRP        7.92e-5 CRP             #>  5 rs10908710 159351189 RS10908710 chr1_1593… CRP        7.92e-5 CRP             #>  6 rs11265178 159359256 RS11265178 chr1_1593… CRP        9.62e-5 CRP             #>  7 rs35532309 159360755 RS35532309 chr1_1593… CRP        6.11e-5 CRP             #>  8 rs6692378  159369451 RS6692378  chr1_1593… CRP        1.17e-6 CRP             #>  9 rs10908714 159370563 RS10908714 chr1_1593… CRP        1.80e-5 CRP             #> 10 rs6656924  159372915 RS6656924  chr1_1593… CRP        1.00e-6 CRP             #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Calculate eQTLs service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"calculate_expression_quantitative_trait_loci(   tissueSiteDetailId,   gencodeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Notes output: Beta standard error recorded columns nes error respectively (see GTEx FAQs) variantId contains (order) chromosome, position, reference allele, alternative allele human genome build separated underscores. reference alternative alleles \"chr1_13550_G_A_b38\" example \"G\" \"\" respectively. See examples calculate minor alternative allele frequencies. Notes input: Argument variantId also accepts RSIDs.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\",                                              gencodeId = \"ENSG00000203782.5\",                                              variantId = \"rs79641866\") #> # A tibble: 1 × 15 #>   data               error gencodeId  geneSymbol genotypes hetCount homoAltCount #>   <list>             <dbl> <chr>      <chr>      <list>       <int>        <int> #> 1 <tibble [670 × 1]> 0.148 ENSG00000… LOR        <tibble>        38            0 #> # ℹ 8 more variables: homoRefCount <int>, maf <dbl>, nes <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, tStatistic <dbl>, tissueSiteDetailId <chr>, #> #   variantId <chr>  # unnest list columns with tidyr::unnest() calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\",                                              gencodeId = \"ENSG00000203782.5\",                                              variantId = \"rs79641866\") |>   tidyr::unnest(c(\"data\", \"genotypes\")) #> # A tibble: 670 × 15 #>      data error gencodeId         geneSymbol genotypes hetCount homoAltCount #>     <dbl> <dbl> <chr>             <chr>          <int>    <int>        <int> #>  1  1.86  0.148 ENSG00000203782.5 LOR                0       38            0 #>  2 -1.06  0.148 ENSG00000203782.5 LOR                0       38            0 #>  3 -0.618 0.148 ENSG00000203782.5 LOR                0       38            0 #>  4 -1.39  0.148 ENSG00000203782.5 LOR                0       38            0 #>  5  0.329 0.148 ENSG00000203782.5 LOR                0       38            0 #>  6  1.37  0.148 ENSG00000203782.5 LOR                0       38            0 #>  7  0.832 0.148 ENSG00000203782.5 LOR                0       38            0 #>  8  0.118 0.148 ENSG00000203782.5 LOR                0       38            0 #>  9  0.197 0.148 ENSG00000203782.5 LOR                0       38            0 #> 10 -0.442 0.148 ENSG00000203782.5 LOR                0       38            0 #> # ℹ 660 more rows #> # ℹ 8 more variables: homoRefCount <int>, maf <dbl>, nes <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, tStatistic <dbl>, tissueSiteDetailId <chr>, #> #   variantId <chr>  # to calculate minor and alternative allele frequencies calculate_expression_quantitative_trait_loci(   tissueSiteDetailId = \"Liver\",   gencodeId = \"ENSG00000237973.1\",   variantId = \"rs12119111\" ) |>  dplyr::bind_rows(.id = \"rsid\") |>   tidyr::separate(    col = \"variantId\",    into = c(      \"chromosome\",      \"position\",      \"reference_allele\",      \"alternative_allele\",      \"genome_build\"    ),    sep = \"_\"  ) |>   # ...then ascertain alternative_allele frequency  dplyr::mutate(    alt_allele_count = (2 * homoAltCount) + hetCount,    total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),    alternative_allele_frequency = alt_allele_count / total_allele_count  ) |>   dplyr::select(    rsid,    beta = nes,    se = error,    pValue,    minor_allele_frequency = maf,    alternative_allele_frequency,    chromosome:genome_build,    tissueSiteDetailId  ) #> # A tibble: 1 × 12 #>   rsid    beta     se pValue minor_allele_frequency alternative_allele_frequency #>   <chr>  <dbl>  <dbl>  <dbl>                  <dbl>                        <dbl> #> 1 1     0.0270 0.0670  0.688                  0.365                        0.635 #> # ℹ 6 more variables: chromosome <chr>, position <chr>, reference_allele <chr>, #> #   alternative_allele <chr>, genome_build <chr>, tissueSiteDetailId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Ieqtls — calculate_ieqtls","title":"Calculate Ieqtls — calculate_ieqtls","text":"Calculate Cell Specific eQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"calculate_ieqtls(   cellType,   tissueSiteDetailId,   gencodeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Ieqtls — calculate_ieqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Ieqtls — calculate_ieqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"# \\dontrun{ # perform request calculate_ieqtls(cellType = \"Adipocytes\",                  tissueSiteDetailId = \"Adipose_Subcutaneous\",                  gencodeId = \"ENSG00000203782.5\",                  variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #>   cellType  data  datasetId enrichmentScores gencodeId genotypes regressionCoord #>   <chr>     <lis> <chr>     <list>           <chr>     <list>    <list>          #> 1 Adipocyt… <dbl> gtex_v8   <dbl [581]>      ENSG0000… <int>     <named list>    #> # ℹ 2 more variables: tissueSiteDetailId <chr>, variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Isqtls — calculate_isqtls","title":"Calculate Isqtls — calculate_isqtls","text":"Calculate Cell Specific sQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"calculate_isqtls(   cellType,   tissueSiteDetailId,   phenotypeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Isqtls — calculate_isqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Isqtls — calculate_isqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"# \\dontrun{ # perform request calculate_isqtls(cellType = \"Neutrophils\",                  tissueSiteDetailId = \"Whole_Blood\",                  phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\",                  variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #>   cellType    data   datasetId enrichmentScores phenotypeId   tissueSiteDetailId #>   <chr>       <list> <chr>     <list>           <chr>         <chr>              #> 1 Neutrophils <dbl>  gtex_v8   <dbl [670]>      chr1:15947:1… Whole_Blood        #> # ℹ 3 more variables: variantId <chr>, genotypes <list>, regressionCoord <list> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"calculate_splicing_quantitative_trait_loci(   tissueSiteDetailId,   phenotypeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_splicing_quantitative_trait_loci(   tissueSiteDetailId = \"Whole_Blood\",   phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\",   variantId = \"chr1_14677_G_A_b38\") #> # A tibble: 1 × 14 #>   data     error genotypes hetCount homoAltCount homoRefCount    maf   nes #>   <list>   <dbl> <list>       <int>        <int>        <int>  <dbl> <dbl> #> 1 <tibble> 0.139 <tibble>        69            0          601 0.0515 0.757 #> # ℹ 6 more variables: pValue <dbl>, pValueThreshold <dbl>, phenotypeId <chr>, #> #   tStatistic <dbl>, tissueSiteDetailId <chr>, variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download — download","title":"Download — download","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download — download","text":"","code":"download(   materialTypes = NULL,   tissueSiteDetailIds = NULL,   pathCategory = NULL,   tissueSampleIds = NULL,   sex = NULL,   sortBy = NULL,   sortDirection = NULL,   searchTerm = NULL,   sampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download — download","text":"materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download — download","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download — download","text":"Note: running request filters (.e. download()) raises error.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download — download","text":"","code":"# \\dontrun{ download(   materialTypes = \"RNA:Total RNA\",   tissueSiteDetailIds = \"Thyroid\",   pathCategory = \"clean_specimens\",   sex = \"male\",   ageBrackets = \"50-59\" ) #> # A tibble: 1 × 26 #>   materialType  sampleId    sampleIdUpper sex     rin hasGTExImage concentration #>   <chr>         <chr>       <chr>         <chr> <dbl> <lgl>                <dbl> #> 1 RNA:Total RNA GTEX-WYJK-… GTEX-WYJK-16… male   7.28 TRUE                  36.4 #> # ℹ 19 more variables: analysisRelease <chr>, genotype <chr>, hardyScale <chr>, #> #   pathologyNotes <chr>, subjectId <chr>, tissueSiteDetailId <chr>, #> #   hasGenotype <lgl>, originalMaterialType <chr>, aliquotId <chr>, #> #   tissueSampleId <chr>, ageBracket <chr>, brainTissueDonor <lgl>, #> #   volume <dbl>, hasExpressionData <lgl>, hasBRDImage <lgl>, #> #   tissueSiteDetail <chr>, pathologyNotesCategories <tibble[,57]>, #> #   amount <dbl>, tissueSite <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotation — get_annotation","title":"Get Annotation — get_annotation","text":"service returns list annotations allowed values particular dataset can subsetted. Results may filtered dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotation — get_annotation","text":"","code":"get_annotation(datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotation — get_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotation — get_annotation","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Annotation — get_annotation","text":"Note: output function appears incomplete currently.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotation — get_annotation","text":"","code":"# \\dontrun{  get_annotation() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 5 #>   entity  values    type  annotation datasetId #>   <chr>   <list>    <chr> <chr>      <chr>     #> 1 subject <chr [2]> enum  sex        gtex_v8   #> 2 subject <chr [6]> enum  ageBracket gtex_v8   # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"Find median transcript expression data along hierarchical clusters. Returns median normalized transcript expression tissues known transcripts given gene along hierarchical clustering results tissues transcripts, based exon expression, Newick format. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"get_clustered_median_exon_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"# \\dontrun{ get_clustered_median_exon_expression(c(\"ENSG00000203782.5\",                                        \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 216 × 8 #>     median exonId   tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #>      <dbl> <chr>    <chr>              <chr>      <chr>     <chr>     <chr>      #>  1  0.789  ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… CRP        #>  2 16.8    ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… CRP        #>  3  0.0921 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… CRP        #>  4 12      ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… CRP        #>  5  1      ENSG000… Adrenal_Gland      UBERON:00… gtex_v8   ENSG0000… CRP        #>  6 22.7    ENSG000… Adrenal_Gland      UBERON:00… gtex_v8   ENSG0000… CRP        #>  7  0      ENSG000… Artery_Aorta       UBERON:00… gtex_v8   ENSG0000… CRP        #>  8  8      ENSG000… Artery_Aorta       UBERON:00… gtex_v8   ENSG0000… CRP        #>  9  0      ENSG000… Artery_Coronary    UBERON:00… gtex_v8   ENSG0000… CRP        #> 10 14      ENSG000… Artery_Coronary    UBERON:00… gtex_v8   ENSG0000… CRP        #> # ℹ 206 more rows #> # ℹ 1 more variable: unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_exon_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $exon #> [1] \"((ENSG00000203782.5_2:8.51,ENSG00000132693.12_2:8.51):0.79,(ENSG00000203782.5_1:5.92,ENSG00000132693.12_1:5.92):3.38);\" #>  #> $tissue #> [1] \"(((((((((((Uterus:0.02,Stomach:0.02):0.04,(Pituitary:0.02,Brain_Cerebellum:0.02):0.04):0.01,((((Thyroid:0.03,Colon_Transverse:0.03):0.00,((Artery_Coronary:0.02,Adipose_Visceral_Omentum:0.02):0.00,(Esophagus_Muscularis:0.01,Esophagus_Gastroesophageal_Junction:0.01):0.01):0.01):0.01,Small_Intestine_Terminal_Ileum:0.04):0.00,Artery_Aorta:0.04):0.03):0.04,Kidney_Cortex:0.11):0.00,Brain_Cerebellar_Hemisphere:0.11):0.02,(((((((Ovary:0.01,Nerve_Tibial:0.01):0.00,Adipose_Subcutaneous:0.01):0.01,Esophagus_Mucosa:0.02):0.01,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.02):0.01,Minor_Salivary_Gland:0.03):0.01,(Prostate:0.02,Lung:0.02):0.02):0.04,Testis:0.09):0.04):0.02,((Fallopian_Tube:0.09,Cervix_Ectocervix:0.09):0.01,((Kidney_Medulla:0.06,Bladder:0.06):0.03,((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.04,Cervix_Endocervix:0.05):0.03):0.02):0.05):0.03,((Vagina:0.09,Brain_Hypothalamus:0.09):0.03,((((((Brain_Hippocampus:0.01,Brain_Amygdala:0.01):0.01,Cells_EBV-transformed_lymphocytes:0.02):0.01,Brain_Frontal_Cortex_BA9:0.02):0.01,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.03):0.02,(Brain_Cortex:0.02,Brain_Anterior_cingulate_cortex_BA24:0.02):0.03):0.02,(((((Brain_Substantia_nigra:0.01,Artery_Tibial:0.01):0.00,(Heart_Atrial_Appendage:0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00):0.00,Muscle_Skeletal:0.01):0.01,Colon_Sigmoid:0.02):0.01,(Whole_Blood:0.02,Heart_Left_Ventricle:0.02):0.02):0.04):0.05):0.06):0.20,Pancreas:0.39):0.34,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.71):0.12,Liver:0.85);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues along hierarchical clustering results tissues genes, based gene expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"get_clustered_median_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"# \\dontrun{ get_clustered_median_gene_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 108 × 7 #>    median tissueSiteDetailId     ontologyId datasetId gencodeId geneSymbol unit  #>     <dbl> <chr>                  <chr>      <chr>     <chr>     <chr>      <chr> #>  1 0.347  Adipose_Subcutaneous   UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  2 0.240  Adipose_Visceral_Omen… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  3 0.384  Adrenal_Gland          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  4 0.198  Artery_Aorta           UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  5 0.332  Artery_Coronary        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  6 0.117  Artery_Tibial          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  7 0.631  Bladder                UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  8 0.0347 Brain_Amygdala         UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 98 more rows  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_gene_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $gene #> [1] \"Not enough data. At least three data sets are required for clustering.\" #>  #> $tissue #> [1] \"(((((((((((Cells_Cultured_fibroblasts:0.01,Bladder:0.01):0.01,Prostate:0.02):0.01,(Testis:0.02,Lung:0.02):0.02):0.01,(((((Thyroid:0.01,Minor_Salivary_Gland:0.01):0.01,Uterus:0.01):0.00,(((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.01,Small_Intestine_Terminal_Ileum:0.01):0.00,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.01):0.01):0.00,((Esophagus_Gastroesophageal_Junction:0.00,Adipose_Visceral_Omentum:0.00):0.00,Esophagus_Muscularis:0.01):0.01):0.01,((Ovary:0.00,Nerve_Tibial:0.00):0.01,Esophagus_Mucosa:0.01):0.02):0.01):0.00,(((((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.00,Colon_Transverse:0.01):0.01,Adrenal_Gland:0.02):0.00,(Kidney_Medulla:0.01,Kidney_Cortex:0.01):0.01):0.02):0.01,((((Whole_Blood:0.01,Heart_Left_Ventricle:0.01):0.01,Brain_Cerebellar_Hemisphere:0.02):0.01,(((Colon_Sigmoid:0.01,Brain_Substantia_nigra:0.01):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.01):0.01):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Amygdala:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.01):0.00,Brain_Anterior_cingulate_cortex_BA24:0.01):0.00,Brain_Hippocampus:0.01):0.01,(Artery_Tibial:0.01,Artery_Aorta:0.01):0.01):0.01):0.02):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Brain_Frontal_Cortex_BA9:0.02):0.03,Vagina:0.05):0.02):0.03,((Cervix_Endocervix:0.02,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.04):0.07):0.10,Pancreas:0.20):0.37,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.07,Liver:0.64);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"Find median junction expression data along hierarchical clusters. Returns median junction read counts tissues given gene known transcripts along hierarchical clustering results tissues genes, based junction expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"get_clustered_median_junction_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"# \\dontrun{ get_clustered_median_junction_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 432 × 8 #>    median junctionId           tissueSiteDetailId ontologyId datasetId gencodeId #>     <dbl> <chr>                <chr>              <chr>      <chr>     <chr>     #>  1      0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  2      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  3      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  4      0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  5      0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  6      0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  7      0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  8      0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #>  9      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> 10      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_junction_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $junction #> [1] \"((((((chr1_159713641_159714006:0.03,chr1_159713604_159714002:0.03):0.67,(chr1_159712795_159714006:0.01,chr1_159712581_159713502:0.01):0.69):0.56,chr1_159712795_159713502:1.26):0.90,chr1_159713973_159714498:2.16):0.54,chr1_159714139_159714424:2.70):2.61,chr1_153259734_153260926:5.31);\" #>  #> $tissue #> [1] \"(((((((((((((((((Adipose_Visceral_Omentum:0.00,Adipose_Subcutaneous:0.00):0.00,Artery_Aorta:0.00):0.00,Artery_Coronary:0.00):0.00,Artery_Tibial:0.00):0.00,Brain_Cortex:0.00):0.00,Breast_Mammary_Tissue:0.00):0.00,Colon_Sigmoid:0.00):0.00,Heart_Atrial_Appendage:0.00):0.00,Muscle_Skeletal:0.00):0.00,Nerve_Tibial:0.00):0.00,Vagina:0.00):0.08,Kidney_Medulla:0.08):0.03,(((((((((((((((((((((Brain_Amygdala:0.00,Bladder:0.00):0.00,Brain_Anterior_cingulate_cortex_BA24:0.00):0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Cerebellar_Hemisphere:0.00):0.00,Brain_Cerebellum:0.00):0.00,Brain_Frontal_Cortex_BA9:0.00):0.00,Brain_Hippocampus:0.00):0.00,Brain_Hypothalamus:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Brain_Substantia_nigra:0.00):0.00,Cells_EBV-transformed_lymphocytes:0.00):0.00,Colon_Transverse:0.00):0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Esophagus_Muscularis:0.00):0.00,Heart_Left_Ventricle:0.00):0.00,Kidney_Cortex:0.00):0.00,Pituitary:0.00):0.00,Thyroid:0.00):0.00,Whole_Blood:0.00):0.11):0.03,((((((((((((Cells_Cultured_fibroblasts:0.00,Adrenal_Gland:0.00):0.00,Esophagus_Mucosa:0.00):0.00,Fallopian_Tube:0.00):0.00,Lung:0.00):0.00,Minor_Salivary_Gland:0.00):0.00,Ovary:0.00):0.00,Prostate:0.00):0.00,Small_Intestine_Terminal_Ileum:0.00):0.00,Spleen:0.00):0.00,Stomach:0.00):0.00,Uterus:0.00):0.06,((Cervix_Endocervix:0.00,Cervix_Ectocervix:0.00):0.00,Testis:0.00):0.06):0.09):0.19,Pancreas:0.33):0.27,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.59):0.68,Liver:1.29);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"Find median transcript expression data known transcripts gene along hierarchical clusters. Returns median normalized expression tissues known transcripts given gene along hierarchical clustering results tissues genes, based expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"get_clustered_median_transcript_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"# \\dontrun{ get_clustered_median_transcript_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 432 × 8 #>    median transcriptId      tissueSiteDetailId    ontologyId datasetId gencodeId #>     <dbl> <chr>             <chr>                 <chr>      <chr>     <chr>     #>  1 0.130  ENST00000255030.9 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  2 0      ENST00000368110.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  3 0      ENST00000368111.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  4 0      ENST00000368112.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  5 0      ENST00000437342.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  6 0.0100 ENST00000473196.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  7 0      ENST00000489317.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #>  9 0      ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> 10 0      ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_transcript_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $transcript #> [1] \"(((ENST00000473196.1:0.46,ENST00000255030.9:0.46):1.64,(((ENST00000437342.1:0.16,ENST00000368112.5:0.16):0.09,(ENST00000368111.5:0.03,ENST00000368110.1:0.03):0.21):0.15,ENST00000489317.1:0.40):1.70):2.76,ENST00000368742.3:4.86);\" #>  #> $tissue #> [1] \"(((((((((((Spleen:0.00,Breast_Mammary_Tissue:0.00):0.01,Lung:0.01):0.00,((Ovary:0.01,Esophagus_Mucosa:0.01):0.00,Nerve_Tibial:0.01):0.01):0.00,((((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.00,Adipose_Visceral_Omentum:0.01):0.00,((Esophagus_Muscularis:0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Thyroid:0.00):0.00):0.00,(Small_Intestine_Terminal_Ileum:0.01,Artery_Aorta:0.01):0.01):0.00):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Hippocampus:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Artery_Tibial:0.01):0.00,Brain_Amygdala:0.01):0.01,(((Brain_Putamen_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,((Colon_Sigmoid:0.00,Brain_Substantia_nigra:0.00):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00):0.01):0.01):0.01,((((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.01,Kidney_Cortex:0.01):0.00,((Uterus:0.01,Prostate:0.01):0.00,Minor_Salivary_Gland:0.01):0.01):0.00,((((Heart_Left_Ventricle:0.01,Colon_Transverse:0.01):0.00,(Whole_Blood:0.00,Brain_Cerebellar_Hemisphere:0.00):0.01):0.00,((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.01):0.00,Kidney_Medulla:0.02):0.01):0.01):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Vagina:0.02):0.01,(Brain_Frontal_Cortex_BA9:0.01,Brain_Anterior_cingulate_cortex_BA24:0.01):0.02):0.03):0.01,((((Cervix_Endocervix:0.02,Bladder:0.02):0.00,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.03):0.02,Testis:0.05):0.01):0.15,Pancreas:0.21):0.36,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.61,Liver:1.19);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"service returns collapsed exons gene model given gene. Gene-level exon-level expression quantification based GENCODE annotation, collapsed single transcript model gene using algorithm developed GTEx analysis team. default, service queries models used latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"get_collapsed_gene_model_exon(   gencodeId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{  get_collapsed_gene_model_exon(gencodeId = \"ENSG00000132693.12\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   featureType       end genomeBuild chromosome exonNumber geneSymbolUpper exonId #>   <chr>           <int> <chr>       <chr>      <chr>      <chr>           <chr>  #> 1 exon        159714589 GRCh38/hg38 chr1       1          CRP             ENSG0… #> 2 exon        159714138 GRCh38/hg38 chr1       2          CRP             ENSG0… #> # ℹ 7 more variables: datasetId <chr>, start <int>, dataSource <chr>, #> #   gencodeId <chr>, geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Dataset Info — get_dataset_info","title":"Get Dataset Info — get_dataset_info","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Dataset Info — get_dataset_info","text":"","code":"get_dataset_info(datasetId = \"gtex_v8\", organizationName = \"GTEx Consortium\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Dataset Info — get_dataset_info","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Dataset Info — get_dataset_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Dataset Info — get_dataset_info","text":"Note: current returns empty values.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Dataset Info — get_dataset_info","text":"","code":"# \\dontrun{ get_dataset_info() #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Downloads Page Data — get_downloads_page_data","title":"Get Downloads Page Data — get_downloads_page_data","text":"Retrieves files belonging given project_id display Downloads Page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"get_downloads_page_data(project_id = \"adult-gtex\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Downloads Page Data — get_downloads_page_data","text":"project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Downloads Page Data — get_downloads_page_data","text":"Tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Downloads Page Data — get_downloads_page_data","text":"Note: GTEx Portal API documentation states \"GTEx currently one project available: gtex\". However, project_id values \"adult-gtex\" \"egtex\" return results, whereas \"gtex\" (see examples).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"# \\dontrun{  # \"adult-gtex\" (default `project_id` value) and \"egtex\" both return results  get_downloads_page_data() #> # A tibble: 9 × 6 #>   name                         displayName description order parent children     #>   <chr>                        <chr>       <chr>       <int> <chr>  <list>       #> 1 gs://adult-gtex/bulk-gex/    Bulk tissu… \"\"              1 gs://… <named list> #> 2 gs://adult-gtex/bulk-qtl/    QTL         \"\"              2 gs://… <named list> #> 3 gs://adult-gtex/single-cell/ Single cell \"\"              3 gs://… <named list> #> 4 gs://adult-gtex/long-read-d… Long read … \"Long Read…     4 gs://… <named list> #> 5 gs://adult-gtex/haplotype-e… Haplotype … \"Haplotype…     5 gs://… <named list> #> 6 gs://adult-gtex/variants/    Variants    \"\"              6 gs://… <named list> #> 7 gs://adult-gtex/references/  Reference   \"\"              7 gs://… <named list> #> 8 gs://adult-gtex/annotations/ Metadata    \"\"              8 gs://… <named list> #> 9 gs://adult-gtex/additional_… Additional… \"\"              9 gs://… <named list>  egtex <- get_downloads_page_data(\"egtex\")  egtex #> # A tibble: 3 × 6 #>   name                    displayName description      order parent children     #>   <chr>                   <chr>       <chr>            <int> <chr>  <list>       #> 1 gs://egtex/methylation/ Methylation \"\"                   1 gs://… <named list> #> 2 gs://egtex/proteomics/  Proteomics  \"Protein and RN…     2 gs://… <named list> #> 3 gs://egtex/telomeres/   Telomeres   \"Relative telom…     3 gs://… <named list>   # ...\"gtex\" does not  get_downloads_page_data(\"gtex\") #> # A tibble: 0 × 0   # get details for whole blood methylation data, including download URL  purrr::pluck(    egtex$children,    1,    \"folders\",    \"Methylation - EPIC Array\",    \"children\",    \"folders\",    \"mQTLs\",    \"children\",    \"files\",    \"WholeBlood.mQTLs.regular.txt.gz\"  ) #> $displayName #> [1] \"WholeBlood.mQTLs.regular.txt.gz\" #>  #> $description #> [1] \"\" #>  #> $fileSize #> [1] 43461408219 #>  #> $url #> [1] \"https://storage.googleapis.com/egtex/methylation/epic-arrays/mQTLs/WholeBlood.mQTLs.regular.txt.gz\" #>  #> $order #> [1] 27 #>  #> $parent #> [1] \"gs://egtex/methylation/epic-arrays/mQTLs/\" #>  # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Eqtl Genes — get_eqtl_genes","title":"Get Eqtl Genes — get_eqtl_genes","text":"Retrieve eGenes (eQTL Genes). service returns eGenes (eQTL Genes) specified dataset. eGenes genes least one significant cis-eQTL acting upon . Results may filtered tissue. default, service queries latest GTEx release. eGene, results include allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), q-value (qValue). log2AllelicFoldChange allelic fold change (log2 scale) significant eQTL. pValue nominal p-value significant eQTL. pValueThreshold p-value threshold used determine whether cis-eQTL gene significant. details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods. empiricalPValue beta distribution-adjusted empirical p-value FastQTL. qValues calculated based empirical p-values. false discovery rate (FDR) threshold <= 0.05 applied identify genes significant eQTL. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"get_eqtl_genes(   tissueSiteDetailIds,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Eqtl Genes — get_eqtl_genes","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Eqtl Genes — get_eqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"# \\dontrun{ get_eqtl_genes(c(\"Whole_Blood\", \"Artery_Aorta\")) #> Warning: ! Total number of items (24853) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 100 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 24853 #> # A tibble: 250 × 10 #>    tissueSiteDetailId ontologyId  datasetId empiricalPValue gencodeId geneSymbol #>    <chr>              <chr>       <chr>               <dbl> <chr>     <chr>      #>  1 Whole_Blood        UBERON:001… gtex_v8          1.05e- 9 ENSG0000… WASH7P     #>  2 Whole_Blood        UBERON:001… gtex_v8          1.06e-25 ENSG0000… RP11-34P1… #>  3 Whole_Blood        UBERON:001… gtex_v8          6.31e- 2 ENSG0000… CICP27     #>  4 Whole_Blood        UBERON:001… gtex_v8          8.71e- 9 ENSG0000… RP11-34P1… #>  5 Whole_Blood        UBERON:001… gtex_v8          6.01e-20 ENSG0000… RP11-34P1… #>  6 Whole_Blood        UBERON:001… gtex_v8          6.96e- 9 ENSG0000… RP11-34P1… #>  7 Whole_Blood        UBERON:001… gtex_v8          3.10e- 4 ENSG0000… RP11-34P1… #>  8 Whole_Blood        UBERON:001… gtex_v8          1.92e- 3 ENSG0000… ABC7-4304… #>  9 Whole_Blood        UBERON:001… gtex_v8          1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood        UBERON:001… gtex_v8          7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, qValue <dbl> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Exons — get_exons","title":"Get Exons — get_exons","text":"service returns exons known transcripts given gene. versioned GENCODE ID required ensure exons single gene. dataset ID GENCODE version genome build must provided. Although annotated exons dataset dependent, specifying dataset equivalent specifying GENCODE version genome build used dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Exons — get_exons","text":"","code":"get_exons(   gencodeId,   gencodeVersion = NULL,   genomeBuild = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Exons — get_exons","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Exons — get_exons","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Exons — get_exons","text":"","code":"# \\dontrun{ get_exons(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #>   featureType       end genomeBuild     start exonId source chromosome gencodeId #>   <chr>           <int> <chr>           <int> <chr>  <chr>  <chr>      <chr>     #> 1 exon        153259733 GRCh38/hg38 153259700 ENSE0… HAVANA chr1       ENSG0000… #> 2 exon        153262122 GRCh38/hg38 153260927 ENSE0… HAVANA chr1       ENSG0000… #> # ℹ 5 more variables: transcriptId <chr>, geneSymbol <chr>, #> #   gencodeVersion <chr>, strand <chr>, exonNumber <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Expression Pca — get_expression_pca","title":"Get Expression Pca — get_expression_pca","text":"Find gene expression PCA data. Returns gene expression PCA (principal component analysis) tissues. Results may filtered tissue, sample, dataset. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Expression Pca — get_expression_pca","text":"","code":"get_expression_pca(   tissueSiteDetailIds,   datasetId = \"gtex_v8\",   sampleId = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Expression Pca — get_expression_pca","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Expression Pca — get_expression_pca","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Expression Pca — get_expression_pca","text":"","code":"# \\dontrun{ get_expression_pca(tissueSiteDetailIds = c(\"Adipose_Subcutaneous\",                                            \"Whole_Blood\")) #> Warning: ! Total number of items (1418) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1418 #> # A tibble: 250 × 7 #>        pc1      pc2      pc3 sampleId    tissueSiteDetailId ontologyId datasetId #>      <dbl>    <dbl>    <dbl> <chr>       <chr>              <chr>      <chr>     #>  1  0.0385 -0.0178   0.0769  GTEX-1117F… Adipose_Subcutane… UBERON:00… gtex_v8   #>  2 -0.0585  0.00809  0.00492 GTEX-111CU… Adipose_Subcutane… UBERON:00… gtex_v8   #>  3  0.140  -0.0308  -0.0368  GTEX-111FC… Adipose_Subcutane… UBERON:00… gtex_v8   #>  4  0.0597  0.140    0.0294  GTEX-111VG… Adipose_Subcutane… UBERON:00… gtex_v8   #>  5 -0.0968  0.00233 -0.0174  GTEX-111YS… Adipose_Subcutane… UBERON:00… gtex_v8   #>  6 -0.120   0.0195  -0.0594  GTEX-1122O… Adipose_Subcutane… UBERON:00… gtex_v8   #>  7 -0.102   0.0652   0.00344 GTEX-1128S… Adipose_Subcutane… UBERON:00… gtex_v8   #>  8  0.105   0.0174  -0.0568  GTEX-113IC… Adipose_Subcutane… UBERON:00… gtex_v8   #>  9 -0.109  -0.0543   0.00594 GTEX-117YX… Adipose_Subcutane… UBERON:00… gtex_v8   #> 10  0.132  -0.0335  -0.0350  GTEX-11DXW… Adipose_Subcutane… UBERON:00… gtex_v8   #> # ℹ 240 more rows  get_expression_pca(tissueSiteDetailIds = \"Adipose_Subcutaneous\",                    sampleId = \"GTEX-1117F-0226-SM-5GZZ7\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #>      pc1     pc2    pc3 sampleId         tissueSiteDetailId ontologyId datasetId #>    <dbl>   <dbl>  <dbl> <chr>            <chr>              <chr>      <chr>     #> 1 0.0385 -0.0178 0.0769 GTEX-1117F-0226… Adipose_Subcutane… UBERON:00… gtex_v8   # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Get File List — get_file_list","title":"Get File List — get_file_list","text":"Get files GTEx dataset Download page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get File List — get_file_list","text":"","code":"get_file_list()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get File List — get_file_list","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get File List — get_file_list","text":"returned tibble includes nested list column, \"filesets\". details files, sub-categorised fileset (see examples section).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get File List — get_file_list","text":"","code":"# \\dontrun{ # Column \"filesets\" is a list column get_file_list() #> # A tibble: 11 × 10 #>    name            subpath dbgapId dataset release order type  id    description #>    <chr>           <chr>   <chr>   <chr>   <chr>   <int> <chr> <chr> <chr>       #>  1 GTEx Analysis … gtex_a… \"phs00… GTEx    v3         10 data… gtex… \"\"          #>  2 GTEx Analysis … gtex_a… \"\"      GTEx    v6p         7 data… gtex… \"The GTEx … #>  3 Biobank Invent… gtex_b… \"\"      GTEx    biobank     5 data… biob… \"\"          #>  4 GTEx Analysis … gtex_a… \"phs00… GTEx    v7          6 data… gtex… \"\"          #>  5 GTEx Analysis … gtex_a… \"phs00… GTEx    v6          8 data… gtex… \"\"          #>  6 Additional Dat… gtex_a… \"\"      GTEx    additi…     3 data… addi… \"\"          #>  7 GTEx Analysis … gtex_a… \"phs00… GTEx    v4          9 data… gtex… \"\"          #>  8 External Datas… gtex_e… \"\"      GTEx    extern…     4 data… exte… \"\"          #>  9 GTEx Analysis … gtex_a… \"phs00… GTEx    v8          1 data… gtex… \"The GTEx … #> 10 eGTEx           gtex_e… \"\"      GTEx    egtex       2 data… egtex \"The Enhan… #> 11 GTEx Analysis … gtex_a… \"phs00… GTEx    v9          0 data… gtex… \"Open-acce… #> # ℹ 1 more variable: filesets <list>  # Get \"GTEx Analysis V9\" file list gtex_v9_files <- get_file_list() |>                    dplyr::filter(name == \"GTEx Analysis V9\") |>                    dplyr::pull(filesets)  # \"GTEx Analysis V9\" filesets names(gtex_v9_files[[1]]) #> [1] \"snRNA-Seq Data\" \"Long Read Data\"  # \"GTEx Analysis V9\", \"snRNA-Seq Data\" fileset files names(gtex_v9_files[[1]][[\"snRNA-Seq Data\"]]$files) #> [1] \"GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad\"        #> [2] \"GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad\" # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Fine Mapping — get_fine_mapping","title":"Get Fine Mapping — get_fine_mapping","text":"Retrieve Fine Mapping Data Finds returns Fine Mapping data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"get_fine_mapping(   gencodeIds,   datasetId = \"gtex_v8\",   variantId = NULL,   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Fine Mapping — get_fine_mapping","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". variantId String. gtex variant ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Fine Mapping — get_fine_mapping","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"# \\dontrun{ # search by gene get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 27 #> # A tibble: 27 × 9 #>    datasetId gencodeId          method     pip setId setSize tissueSiteDetailId #>    <chr>     <chr>              <chr>    <dbl> <int>   <int> <chr>              #>  1 gtex_v8   ENSG00000132693.12 DAP-G  0.0235      1       5 Thyroid            #>  2 gtex_v8   ENSG00000132693.12 DAP-G  0.0221      1       5 Thyroid            #>  3 gtex_v8   ENSG00000132693.12 DAP-G  0.0171      1       5 Thyroid            #>  4 gtex_v8   ENSG00000132693.12 DAP-G  0.0252      1       5 Thyroid            #>  5 gtex_v8   ENSG00000132693.12 DAP-G  0.892       1       5 Thyroid            #>  6 gtex_v8   ENSG00000203782.5  DAP-G  0.0126      1      22 Whole_Blood        #>  7 gtex_v8   ENSG00000203782.5  DAP-G  0.00690     1      22 Whole_Blood        #>  8 gtex_v8   ENSG00000203782.5  DAP-G  0.0313      1      22 Whole_Blood        #>  9 gtex_v8   ENSG00000203782.5  DAP-G  0.00852     1      22 Whole_Blood        #> 10 gtex_v8   ENSG00000203782.5  DAP-G  0.0105      1      22 Whole_Blood        #> # ℹ 17 more rows #> # ℹ 2 more variables: ontologyId <chr>, variantId <chr>  # optionally filter for a single variant and/or one or more tissues get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\"),                  variantId = \"chr1_153228363_A_G_b38\",                  tissueSiteDetailIds = c(\"Whole_Blood\",                                         \"Thyroid\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 9 #>   datasetId gencodeId  method    pip setId setSize tissueSiteDetailId ontologyId #>   <chr>     <chr>      <chr>   <dbl> <int>   <int> <chr>              <chr>      #> 1 gtex_v8   ENSG00000… DAP-G  0.0126     1      22 Whole_Blood        UBERON:00… #> # ℹ 1 more variable: variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"service allows user query full Collapsed Gene Model Exon specific gene gencode ID GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"get_full_get_collapsed_gene_model_exon(gencodeId, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{   get_full_get_collapsed_gene_model_exon(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   featureType       end genomeBuild chromosome exonNumber geneSymbolUpper exonId #>   <chr>           <int> <chr>       <chr>      <chr>      <chr>           <chr>  #> 1 exon        153259733 GRCh38/hg38 chr1       1          LOR             ENSG0… #> 2 exon        153262122 GRCh38/hg38 chr1       2          LOR             ENSG0… #> # ℹ 7 more variables: datasetId <chr>, start <int>, dataSource <chr>, #> #   gencodeId <chr>, geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Functional Annotation — get_functional_annotation","title":"Get Functional Annotation — get_functional_annotation","text":"endpoint retrieves functional annotation certain chromosome location. Default recent dataset release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"get_functional_annotation(   datasetId = \"gtex_v8\",   chromosome,   start,   end,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Functional Annotation — get_functional_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". start Integer. end Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Functional Annotation — get_functional_annotation","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"# \\dontrun{   get_functional_annotation(chromosome = \"chr1\", start = 192168000, end = 192169000) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3 #> # A tibble: 3 × 23 #>   variantId         enhancer promoter openChromatinRegion promoterFlankingRegion #>   <chr>             <lgl>    <lgl>    <lgl>               <lgl>                  #> 1 chr1_192168015_T… TRUE     FALSE    FALSE               FALSE                  #> 2 chr1_192168266_T… TRUE     FALSE    FALSE               FALSE                  #> 3 chr1_192168728_T… FALSE    FALSE    FALSE               FALSE                  #> # ℹ 18 more variables: ctcfBindingSite <lgl>, tfBindingSite <lgl>, #> #   `3PrimeUtrVariant` <lgl>, `5PrimeUtrVariant` <lgl>, #> #   frameshiftVariant <lgl>, intronVariant <lgl>, missenseVariant <lgl>, #> #   nonCodingTranscriptExonVariant <lgl>, spliceAcceptorVariant <lgl>, #> #   spliceDonorVariant <lgl>, spliceRegionVariant <lgl>, stopGained <lgl>, #> #   synonymousVariant <lgl>, chromosome <chr>, pos <int>, ref <chr>, alt <chr>, #> #   datasetId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Expression — get_gene_expression","title":"Get Gene Expression — get_gene_expression","text":"Find normalized gene expression data. Returns normalized gene expression tissues sample level. Results may filtered dataset, gene tissue, least one gene must provided. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Expression — get_gene_expression","text":"","code":"get_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   attributeSubset = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Expression — get_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Expression — get_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Expression — get_gene_expression","text":"","code":"# \\dontrun{   # multiple genes, selected tissues   get_gene_expression(gencodeIds = c(\"ENSG00000132693.12\",                                      \"ENSG00000203782.5\"),                       tissueSiteDetailIds = c(\"Thyroid\", \"Whole_Blood\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… LOR        TPM   #> 2 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… LOR        TPM   #> 3 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 4 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <lgl>    # single gene, selected (single) tissue   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <lgl>    # subset by sex   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\",                       attributeSubset = \"sex\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 2 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [501]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 2 <dbl [254]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <chr>    # subset by age bracket   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\",                       attributeSubset = \"ageBracket\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 6 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [68]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 2 <dbl [68]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 3 <dbl [113]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 4 <dbl [234]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 5 <dbl [249]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 6 <dbl [23]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Search — get_gene_search","title":"Get Gene Search — get_gene_search","text":"Find genes partial complete match gene_id gene_id gene symbol, gencode ID, Ensemble ID Gencode Version Genome Build must specified GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Search — get_gene_search","text":"","code":"get_gene_search(   geneId,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Search — get_gene_search","text":"geneId String. gene symbol, gencode ID, Ensemble ID. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Search — get_gene_search","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Search — get_gene_search","text":"","code":"# \\dontrun{ get_gene_search(\"CRP\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #>   chromosome dataSource description      end gencodeId gencodeVersion geneStatus #>   <chr>      <chr>      <chr>          <int> <chr>     <chr>          <chr>      #> 1 chr1       HAVANA     C-reactive p… 1.60e8 ENSG0000… v26            \"\"         #> 2 chr1       HAVANA     C-reactive p… 1.60e8 ENSG0000… v26            \"\"         #> # ℹ 8 more variables: geneSymbol <chr>, geneSymbolUpper <chr>, geneType <chr>, #> #   genomeBuild <chr>, start <int>, strand <chr>, tss <int>, entrezGeneId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genes — get_genes","title":"Get Genes — get_genes","text":"service returns information reference genes. genome build GENCODE version must provided. Genes searchable gene symbol, GENCODE ID versioned GENCODE ID. Versioned GENCODE ID recommended ensure unique ID matching. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genes — get_genes","text":"","code":"get_genes(   geneIds,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genes — get_genes","text":"geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genes — get_genes","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genes — get_genes","text":"","code":"# \\dontrun{ get_genes(c(\"CRP\", \"IL6R\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #>   chromosome dataSource description    end entrezGeneId gencodeId gencodeVersion #>   <chr>      <chr>      <chr>        <int> <chr>        <chr>     <chr>          #> 1 chr1       HAVANA     interleuki… 1.54e8 3570         ENSG0000… v26            #> 2 chr1       HAVANA     C-reactive… 1.60e8 1401         ENSG0000… v26            #> # ℹ 8 more variables: geneStatus <chr>, geneSymbol <chr>, #> #   geneSymbolUpper <chr>, geneType <chr>, genomeBuild <chr>, start <int>, #> #   strand <chr>, tss <int> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genomic Features — get_genomic_features","title":"Get Genomic Features — get_genomic_features","text":"GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genomic Features — get_genomic_features","text":"","code":"get_genomic_features(.featureId, datasetId = \"gtex_v8\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genomic Features — get_genomic_features","text":".featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genomic Features — get_genomic_features","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Genomic Features — get_genomic_features","text":"endpoint takes path parameter \"featureId\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genomic Features — get_genomic_features","text":"","code":"# \\dontrun{ # gene symbol get_genomic_features(\"brca1\") #> # A tibble: 1 × 17 #>   gencodeVersion      end description     geneSymbolUpper genomeBuild geneStatus #>   <chr>             <int> <chr>           <chr>           <chr>       <chr>      #> 1 v26            43170245 BRCA1, DNA rep… BRCA1           GRCh38/hg38 \"\"         #> # ℹ 11 more variables: strand <chr>, entrezGeneId <int>, geneType <chr>, #> #   start <int>, dataSource <chr>, gencodeId <chr>, geneSymbol <chr>, #> #   tss <int>, chromosome <chr>, featureType <chr>, assembly <chr>  # GENCODE ID get_genomic_features(\"ENSG00000132693.12\") #> # A tibble: 1 × 17 #>   gencodeVersion       end description    geneSymbolUpper genomeBuild geneStatus #>   <chr>              <int> <chr>          <chr>           <chr>       <chr>      #> 1 v26            159714589 C-reactive pr… CRP             GRCh38/hg38 \"\"         #> # ℹ 11 more variables: strand <chr>, entrezGeneId <int>, geneType <chr>, #> #   start <int>, dataSource <chr>, gencodeId <chr>, geneSymbol <chr>, #> #   tss <int>, chromosome <chr>, featureType <chr>, assembly <chr>  # RSID get_genomic_features(\"rs1815739\") #> # A tibble: 1 × 8 #>   featureType chromosome    start snpId     variantId       ref   alt   assembly #>   <chr>       <chr>         <int> <chr>     <chr>           <chr> <chr> <chr>    #> 1 snp         chr11      66560624 rs1815739 chr11_66560624… C     T     HG38      # GTEx variant ID get_genomic_features(\"chr11_66561023_G_GTTA_b38\") #> # A tibble: 1 × 8 #>   featureType chromosome    start snpId     variantId       ref   alt   assembly #>   <chr>       <chr>         <int> <chr>     <chr>           <chr> <chr> <chr>    #> 1 snp         chr11      66561023 rs3837428 chr11_66561023… G     GTTA  HG38     # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"Find GWAS Catalog certain chromosome start end locations. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"get_gwas_catalog_by_location(   start,   end,   chromosome,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"# \\dontrun{ get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = \"chr1\") #> Warning: ! Total number of items (316) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 316 #> # A tibble: 250 × 10 #>    chromosome   start     end phenotype  pValue   beta pubmedId snpId riskAllele #>    <chr>        <int>   <int> <chr>       <dbl>  <dbl>    <int> <chr> <chr>      #>  1 chr1       9653328 9653329 Testicula…  6e-13 1.14   28604728 rs42… T          #>  2 chr1       8428505 8428506 Autism sp…  7e- 9 1.06   28540026 rs30… ?          #>  3 chr1       9651584 9651585 Monocyte …  2e- 9 0.0222 27863252 rs75… G          #>  4 chr1       3080038 3080039 Mean corp…  1e-13 0.0311 27863252 rs15… C          #>  5 chr1       3811497 3811498 Mean corp…  1e-13 0.0301 27863252 rs12… T          #>  6 chr1       4544044 4544045 Adolescen…  3e- 9 1.2    26394188 rs24… ?          #>  7 chr1       1312114 1312115 Inflammat…  8e-13 1.10   23128233 rs12… A          #>  8 chr1       7961913 7961914 Inflammat…  1e-15 1.11   23128233 rs35… G          #>  9 chr1       8444361 8444362 Eosinophi…  2e-19 0.0328 27863252 rs15… A          #> 10 chr1       9281727 9281728 Eosinophi…  1e-10 0.0260 27863252 rs67… T          #> # ℹ 240 more rows #> # ℹ 1 more variable: genomeBuild <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Image — get_image","title":"Get Image — get_image","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Image — get_image","text":"","code":"get_image(tissueSampleIds = NULL, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Image — get_image","text":"tissueSampleIds Array strings. list Tissue Sample ID(s). page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Image — get_image","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Image — get_image","text":"","code":"# \\dontrun{ get_image() #> Warning: ! Total number of items (25713) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 103 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25713 #> # A tibble: 250 × 11 #>    ageBracket hardyScale hide  histologyImageId pathologyNotes   sex   subjectId #>    <chr>      <chr>      <lgl> <chr>            <chr>            <chr> <chr>     #>  1 60-69      Slow death FALSE GTEX-1117F-0126  6 pieces, minim… fema… GTEX-111… #>  2 60-69      Slow death FALSE GTEX-1117F-0226  2 pieces, ~15% … fema… GTEX-111… #>  3 60-69      Slow death FALSE GTEX-1117F-0326  2 pieces, clean… fema… GTEX-111… #>  4 60-69      Slow death FALSE GTEX-1117F-0426  2 pieces, !5% f… fema… GTEX-111… #>  5 60-69      Slow death FALSE GTEX-1117F-0526  2 pieces, clean… fema… GTEX-111… #>  6 60-69      Slow death FALSE GTEX-1117F-0626  2 pieces, up to… fema… GTEX-111… #>  7 60-69      Slow death FALSE GTEX-1117F-0726  2 pieces, no ab… fema… GTEX-111… #>  8 60-69      Slow death FALSE GTEX-1117F-0826  2 pieces, exten… fema… GTEX-111… #>  9 60-69      Slow death FALSE GTEX-1117F-0926  6 pieces, adher… fema… GTEX-111… #> 10 60-69      Slow death FALSE GTEX-1117F-1026  2 pieces, moder… fema… GTEX-111… #> # ℹ 240 more rows #> # ℹ 4 more variables: tissueSiteDetail <chr>, sampleId <chr>, #> #   tissueSampleId <chr>, pathologyNotesCategories <tibble[,31]>  # filter by `tissueSampleId` result <- get_image(tissueSampleIds = \"GTEX-1117F-0526\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 print(result) #> # A tibble: 1 × 11 #>   ageBracket hardyScale hide  histologyImageId pathologyNotes                    #>   <chr>      <chr>      <lgl> <chr>            <chr>                             #> 1 60-69      Slow death FALSE GTEX-1117F-0526  2 pieces, clean, Monckebeg media… #> # ℹ 6 more variables: pathologyNotesCategories <tibble[,2]>, sampleId <chr>, #> #   sex <chr>, subjectId <chr>, tissueSampleId <chr>, tissueSiteDetail <chr>  # note that `pathologyNotesCategories` (if present) is a list column print(result$pathologyNotesCategories) #> # A tibble: 1 × 2 #>   monckeberg sclerotic #>   <lgl>      <lgl>     #> 1 TRUE       TRUE      # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Independent Eqtl — get_independent_eqtl","title":"Get Independent Eqtl — get_independent_eqtl","text":"Retrieve Independent eQTL Data Finds returns Independent eQTL Data data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"get_independent_eqtl(   gencodeIds,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Independent Eqtl — get_independent_eqtl","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Independent Eqtl — get_independent_eqtl","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"# \\dontrun{ # search by gene get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 8 #> # A tibble: 8 × 14 #>   gencodeId       geneSymbol variantId snpId tissueSiteDetailId ontologyId  rank #>   <chr>           <chr>      <chr>     <chr> <chr>              <chr>      <int> #> 1 ENSG0000013269… CRP        chr1_160… rs66… Esophagus_Gastroe… UBERON:00…     1 #> 2 ENSG0000013269… CRP        chr1_159… rs57… Thyroid            UBERON:00…     1 #> 3 ENSG0000020378… LOR        chr1_153… rs14… Artery_Coronary    UBERON:00…     1 #> 4 ENSG0000020378… LOR        chr1_153… rs87… Whole_Blood        UBERON:00…     1 #> 5 ENSG0000020378… LOR        chr1_153… rs12… Skin_Sun_Exposed_… UBERON:00…     1 #> 6 ENSG0000020378… LOR        chr1_152… rs77… Heart_Atrial_Appe… UBERON:00…     1 #> 7 ENSG0000020378… LOR        chr1_153… rs12… Esophagus_Mucosa   UBERON:00…     1 #> 8 ENSG0000013269… CRP        chr1_159… rs86… Muscle_Skeletal    UBERON:00…     1 #> # ℹ 7 more variables: tssDistance <int>, maf <dbl>, pValue <dbl>, nes <dbl>, #> #   chromosome <chr>, pos <int>, datasetId <chr>  # optionally filter for a single variant and/or one or more tissues get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\",                                     \"ENSG00000203782.5\"),                      tissueSiteDetailIds = c(\"Whole_Blood\",                                              \"Thyroid\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   gencodeId       geneSymbol variantId snpId tissueSiteDetailId ontologyId  rank #>   <chr>           <chr>      <chr>     <chr> <chr>              <chr>      <int> #> 1 ENSG0000013269… CRP        chr1_159… rs57… Thyroid            UBERON:00…     1 #> 2 ENSG0000020378… LOR        chr1_153… rs87… Whole_Blood        UBERON:00…     1 #> # ℹ 7 more variables: tssDistance <int>, maf <dbl>, pValue <dbl>, nes <dbl>, #> #   chromosome <chr>, pos <int>, datasetId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"Find linkage disequilibrium (LD) data given variant GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(   variantId,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"variantId String. gtex variant ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(\"chr1_159245536_C_T_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 241 #> # A tibble: 241 × 3 #>    variantId_1             variantId_2               ld #>    <chr>                   <chr>                  <dbl> #>  1 chr1_159163610_GA_G_b38 chr1_159245536_C_T_b38 0.114 #>  2 chr1_159163924_G_A_b38  chr1_159245536_C_T_b38 0.114 #>  3 chr1_159164864_T_C_b38  chr1_159245536_C_T_b38 0.114 #>  4 chr1_159165054_A_G_b38  chr1_159245536_C_T_b38 0.113 #>  5 chr1_159165563_T_C_b38  chr1_159245536_C_T_b38 0.113 #>  6 chr1_159174791_T_C_b38  chr1_159245536_C_T_b38 0.252 #>  7 chr1_159176518_G_T_b38  chr1_159245536_C_T_b38 0.146 #>  8 chr1_159176900_C_A_b38  chr1_159245536_C_T_b38 0.271 #>  9 chr1_159177147_A_T_b38  chr1_159245536_C_T_b38 0.274 #> 10 chr1_159179691_T_C_b38  chr1_159245536_C_T_b38 0.253 #> # ℹ 231 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"Find linkage disequilibrium (LD) data given gene. endpoint returns linkage disequilibrium data cis-eQTLs found associated provided gene specified dataset. Results queried gencode ID. default, service queries latest GTEx release. Specify dataset ID fetch results different dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(   gencodeId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(gencodeId = \"ENSG00000132693.12\") #> Warning: ! Total number of items (3558) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 15 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3558 #> # A tibble: 250 × 3 #>    variantId_1            variantId_2                         ld #>    <chr>                  <chr>                            <dbl> #>  1 chr1_159230230_G_T_b38 chr1_159230339_A_C_b38           1     #>  2 chr1_159230230_G_T_b38 chr1_159245536_C_T_b38           0.971 #>  3 chr1_159230230_G_T_b38 chr1_159302270_T_C_b38           0.717 #>  4 chr1_159230230_G_T_b38 chr1_159343657_A_T_b38           0.302 #>  5 chr1_159230230_G_T_b38 chr1_159344052_G_A_b38           0.300 #>  6 chr1_159230230_G_T_b38 chr1_159347493_G_A_b38           0.300 #>  7 chr1_159230230_G_T_b38 chr1_159350390_C_A_b38           0.300 #>  8 chr1_159230230_G_T_b38 chr1_159351189_G_A_b38           0.300 #>  9 chr1_159230230_G_T_b38 chr1_159359256_C_A_b38           0.302 #> 10 chr1_159230230_G_T_b38 chr1_159360755_ATACATAAGTG_A_b38 0.300 #> # ℹ 240 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Maintenance Message — get_maintenance_message","title":"Get Maintenance Message — get_maintenance_message","text":"Getting maintenance messages database enabled. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"get_maintenance_message(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Maintenance Message — get_maintenance_message","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Maintenance Message — get_maintenance_message","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Maintenance Message — get_maintenance_message","text":"Note typically returns empty tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"# \\dontrun{ get_maintenance_message() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 0 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 0 #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Exon Expression — get_median_exon_expression","title":"Get Median Exon Expression — get_median_exon_expression","text":"Find median exon expression data. Returns median exon read counts, tissues, collapsed gene model. Results may filtered dataset, gene tissue, least one gene must provided default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"get_median_exon_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Exon Expression — get_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Exon Expression — get_median_exon_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"# \\dontrun{ # median exon expression values for CRP, filtered for whole blood get_median_exon_expression(gencodeIds = \"ENSG00000132693.12\",                            tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 8 #>   median exonId     tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #>    <dbl> <chr>      <chr>              <chr>      <chr>     <chr>     <chr>      #> 1      0 ENSG00000… Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        #> 2      5 ENSG00000… Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        #> # ℹ 1 more variable: unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Gene Expression — get_median_gene_expression","title":"Get Median Gene Expression — get_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"get_median_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Gene Expression — get_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Gene Expression — get_median_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"# \\dontrun{ get_median_gene_expression(gencodeIds = \"ENSG00000132693.12\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 7 #>    median tissueSiteDetailId     ontologyId datasetId gencodeId geneSymbol unit  #>     <dbl> <chr>                  <chr>      <chr>     <chr>     <chr>      <chr> #>  1 0.347  Adipose_Subcutaneous   UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  2 0.240  Adipose_Visceral_Omen… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  3 0.384  Adrenal_Gland          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  4 0.198  Artery_Aorta           UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  5 0.332  Artery_Coronary        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  6 0.117  Artery_Tibial          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  7 0.631  Bladder                UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  8 0.0347 Brain_Amygdala         UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 44 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Junction Expression — get_median_junction_expression","title":"Get Median Junction Expression — get_median_junction_expression","text":"Find junction gene expression data. Returns median junction read counts tissues given gene known transcripts. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"get_median_junction_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Junction Expression — get_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Junction Expression — get_median_junction_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"# \\dontrun{ get_median_junction_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #>    median junctionId           tissueSiteDetailId ontologyId datasetId gencodeId #>     <dbl> <chr>                <chr>              <chr>      <chr>     <chr>     #>  1      0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  2      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  3      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  4      0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  5      0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  6      0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  7      0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  8      0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #>  9      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> 10      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Transcript Expression — get_median_transcript_expression","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"Find median transcript expression data known transcripts gene. Returns median normalized expression tissues known transcripts given gene. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"get_median_transcript_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"# \\dontrun{ get_median_transcript_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #>    median transcriptId      tissueSiteDetailId    ontologyId datasetId gencodeId #>     <dbl> <chr>             <chr>                 <chr>      <chr>     <chr>     #>  1 0.130  ENST00000255030.9 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  2 0      ENST00000368110.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  3 0      ENST00000368111.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  4 0      ENST00000368112.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  5 0      ENST00000437342.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  6 0.0100 ENST00000473196.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  7 0      ENST00000489317.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #>  9 0      ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> 10 0      ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"Find multi-tissue eQTL Metasoft results. service returns multi-tissue eQTL Metasoft results given gene variant specified dataset. Versioned GENCODE ID must provided. tissue, results include: m-value (mValue), normalized effect size (nes), p-value (pValue), standard error (se). m-value posterior probability eQTL effect exists tissue tested cross-tissue meta-analysis (Han Eskin, PLoS Genetics 8(3): e1002555, 2012). normalized effect size slope linear regression normalized expression data versus three genotype categories using single-tissue eQTL analysis, representing eQTL effect size. p-value t-test compares observed NES single-tissue eQTL analysis null NES 0. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"get_multi_tissue_eqtls(   gencodeIds,   variantId = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_multi_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\",                                      \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 132 #> # A tibble: 6,468 × 5 #>    gencodeId         datasetId   metaP variantId              tissues          #>    <chr>             <chr>       <dbl> <chr>                  <named list>     #>  1 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  2 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  3 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  4 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  5 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  6 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  7 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  8 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  9 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #> 10 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #> # ℹ 6,458 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Neighbor Gene — get_neighbor_gene","title":"Get Neighbor Gene — get_neighbor_gene","text":"Find neighboring genes certain chromosome around position certain window size. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"get_neighbor_gene(pos, chromosome, bp_window, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Neighbor Gene — get_neighbor_gene","text":"pos Integer, vector. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". bp_window Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Neighbor Gene — get_neighbor_gene","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"# \\dontrun{ get_neighbor_gene(pos = 1000000, chromosome = \"chr1\", bp_window = 10000) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 15 #>   chromosome dataSource description      end gencodeId gencodeVersion geneStatus #>   <chr>      <chr>      <chr>          <int> <chr>     <chr>          <chr>      #> 1 chr1       HAVANA     novel transc… 9.98e5 ENSG0000… v26            \"\"         #> 2 chr1       HAVANA     hes family b… 1.00e6 ENSG0000… v26            \"\"         #> 3 chr1       HAVANA     ISG15 ubiqui… 1.01e6 ENSG0000… v26            \"\"         #> 4 chr1       HAVANA     ribosomal pr… 1.01e6 ENSG0000… v26            \"\"         #> # ℹ 8 more variables: geneSymbol <chr>, geneSymbolUpper <chr>, geneType <chr>, #> #   genomeBuild <chr>, start <int>, strand <chr>, tss <int>, entrezGeneId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":null,"dir":"Reference","previous_headings":"","what":"Get News Item — get_news_item","title":"Get News Item — get_news_item","text":"Getting news items database current. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get News Item — get_news_item","text":"","code":"get_news_item(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get News Item — get_news_item","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get News Item — get_news_item","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get News Item — get_news_item","text":"","code":"# \\dontrun{ get_news_item() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 23 #> # A tibble: 23 × 6 #>    title                                newsText  rank dateCreated release    id #>    <chr>                                <chr>    <int> <chr>       <chr>   <int> #>  1 New Top 50 Expressed Genes Visualiz… \"The GT…   240 2018-04-04  news_i…   240 #>  2 New Multi-Gene Query Visualization   \"The GT…   250 2018-04-04  news_i…   250 #>  3 New eQTL Dashboard Visualization     \"The GT…   260 2018-04-04  news_i…   260 #>  4 Video Tutorial for the Gene-eQTL Vi… \"Watch …   270 2018-04-05  news_i…   270 #>  5 Access GTEx Biospecimens Here        \"We hav…   280 2018-05-10  news_i…   280 #>  6 Access GTEx Data Programmatically w… \"You ca…   290 2018-09-20  news_i…   290 #>  7 Reuse GTEx Visualizations On Your W… \"You ca…   300 2018-09-20  news_i…   300 #>  8 Use The GTEx Portal On Your Phone    \"We hav…   310 2018-09-20  news_i…   310 #>  9 GTEx Portal Visualizations Updated   \"We hav…   320 2018-12-06  news_i…   320 #> 10 Help Us Help You: New Feature Survey \"PLEASE…   331 2019-02-06  news_i…   331 #> # ℹ 13 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Biobank Data) — get_sample_biobank_data","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"get_sample_biobank_data(   draw = NULL,   materialTypes = NULL,   tissueSiteDetailIds = NULL,   pathCategory = NULL,   tissueSampleIds = NULL,   sex = NULL,   sortBy = \"sampleId\",   sortDirection = \"asc\",   searchTerm = NULL,   sampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"draw Integer. materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"# \\dontrun{  get_sample_biobank_data(tissueSiteDetailIds = \"Whole_Blood\") #> Warning: ! Total number of items (1329) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems (recordsFiltered) = 1329 #> • recordsTotal = 72513 #> # A tibble: 250 × 26 #>    materialType    sampleId       sampleIdUpper sex   hasGTExImage concentration #>    <chr>           <chr>          <chr>         <chr> <lgl>                <dbl> #>  1 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               190.   #>  2 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               154    #>  3 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE                41.2  #>  4 DNA:DNA Genomic GTEX-111CU-00… GTEX-111CU-0… male  FALSE                85.9  #>  5 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                96.0  #>  6 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                95.3  #>  7 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE               142.   #>  8 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE                 4.35 #>  9 RNA:Total RNA   GTEX-111FC-00… GTEX-111FC-0… male  FALSE               128.   #> 10 RNA:Total RNA   GTEX-111FC-00… GTEX-111FC-0… male  FALSE               128.   #> # ℹ 240 more rows #> # ℹ 20 more variables: analysisRelease <chr>, genotype <chr>, hardyScale <chr>, #> #   pathologyNotes <chr>, subjectId <chr>, tissueSiteDetailId <chr>, #> #   hasGenotype <lgl>, originalMaterialType <chr>, aliquotId <chr>, #> #   tissueSampleId <chr>, ageBracket <chr>, brainTissueDonor <lgl>, #> #   volume <dbl>, hasExpressionData <lgl>, hasBRDImage <lgl>, #> #   tissueSiteDetail <chr>, amount <dbl>, mass <dbl>, tissueSite <chr>, … # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"service returns information samples used analyses datasets. Results may filtered dataset ID, sample ID, subject ID, sample metadata, provided parameters. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"get_sample_datasets_endpoints(   datasetId = \"gtex_v8\",   sampleIds = NULL,   tissueSampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   sex = NULL,   pathCategory = NULL,   tissueSiteDetailId = NULL,   aliquotIds = NULL,   autolysisScores = NULL,   hardyScales = NULL,   ischemicTime = NULL,   ischemicTimeGroups = NULL,   rin = NULL,   uberonIds = NULL,   dataTypes = NULL,   sortBy = NULL,   sortDirection = NULL,   page = NULL,   itemsPerPage = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleIds Character vector. GTEx sample ID. tissueSampleIds Array strings. list Tissue Sample ID(s). subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". sex String. Options: \"male\", \"female\". pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. aliquotIds Character vector. autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". rin Integer vector. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"# \\dontrun{  get_sample_datasets_endpoints() #> Warning: ! Total number of items (22734) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 91 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 22734 #> # A tibble: 10,946 × 20 #>    ischemicTime aliquotId tissueSampleId       tissueSiteDetail         dataType #>           <int> <chr>     <chr>                <chr>                    <chr>    #>  1         1188 SM-58Q7G  GTEX-1117F-0003      Whole Blood              WES      #>  2         1188 SM-5DWSB  GTEX-1117F-0003      Whole Blood              OMNI     #>  3         1188 SM-6WBT7  GTEX-1117F-0003      Whole Blood              WGS      #>  4         1193 SM-AHZ7F  GTEX-1117F-0011-R10a Brain - Frontal Cortex … NA       #>  5         1193 SM-CYKQ8  GTEX-1117F-0011-R10b Brain - Frontal Cortex … NA       #>  6         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  7         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  8         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  9         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #> 10         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #> # ℹ 10,936 more rows #> # ℹ 15 more variables: ischemicTimeGroup <chr>, freezeType <chr>, #> #   sampleId <chr>, sampleIdUpper <chr>, ageBracket <chr>, hardyScale <chr>, #> #   tissueSiteDetailId <chr>, subjectId <chr>, uberonId <chr>, sex <chr>, #> #   datasetId <chr>, rin <chr>, pathologyNotesCategories <named list>, #> #   pathologyNotes <chr>, autolysisScore <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Service Info — get_service_info","title":"Get Service Info — get_service_info","text":"General information GTEx service. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Service Info — get_service_info","text":"","code":"get_service_info()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Service Info — get_service_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Service Info — get_service_info","text":"","code":"# \\dontrun{ get_service_info() #> # A tibble: 1 × 9 #>   id     name  version organization_name organization_url description contactUrl #>   <chr>  <chr> <chr>   <chr>             <chr>            <chr>       <chr>      #> 1 org.g… GTEx… 2.0.0   GTEx Project      https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl <chr>, environment <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Find significant single tissue eQTLs. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, gene, variant dataset. search gene, use versioned GENCODE ID. search variant, use dbSNP rs ID (snpId). default, service queries latest GTEx release retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"get_significant_single_tissue_eqtls(   gencodeIds = NULL,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Note: although GTEx Portal API documentation says use dbSNP rsID searching variant, returns results. Instead use gtex variant IDs e.g. use \"chr1_153209640_C_A_b38\" instead \"rs1410858\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs12128960 159343657 RS12128960 chr1_1593… CRP        8.52e-5 CRP             #>  2 rs12132451 159344052 RS12132451 chr1_1593… CRP        7.92e-5 CRP             #>  3 rs12136402 159347493 RS12136402 chr1_1593… CRP        7.92e-5 CRP             #>  4 rs10908709 159350390 RS10908709 chr1_1593… CRP        7.92e-5 CRP             #>  5 rs10908710 159351189 RS10908710 chr1_1593… CRP        7.92e-5 CRP             #>  6 rs11265178 159359256 RS11265178 chr1_1593… CRP        9.62e-5 CRP             #>  7 rs35532309 159360755 RS35532309 chr1_1593… CRP        6.11e-5 CRP             #>  8 rs6692378  159369451 RS6692378  chr1_1593… CRP        1.17e-6 CRP             #>  9 rs10908714 159370563 RS10908714 chr1_1593… CRP        1.80e-5 CRP             #> 10 rs6656924  159372915 RS6656924  chr1_1593… CRP        1.00e-6 CRP             #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>  # search by variant - must be variantId (not rsid) get_significant_single_tissue_eqtls(variantIds = \"chr1_153209640_C_A_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #>   snpId           pos snpIdUpper variantId   geneSymbol   pValue geneSymbolUpper #>   <chr>         <int> <chr>      <chr>       <chr>         <dbl> <chr>           #> 1 rs1410858 153209640 RS1410858  chr1_15320… LOR        5.47e- 5 LOR             #> 2 rs1410858 153209640 RS1410858  chr1_15320… PRR9       5.35e-19 PRR9            #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>  # filter by gene/variant and tissue site - either `gencodeIds` or `variantIds` # should be supplied as a minimum get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\"),                                     variantIds = \"chr1_153209640_C_A_b38\",                                     tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 13 #>   snpId    pos snpIdUpper variantId geneSymbol  pValue geneSymbolUpper datasetId #>   <chr>  <int> <chr>      <chr>     <chr>        <dbl> <chr>           <chr>     #> 1 rs14… 1.53e8 RS1410858  chr1_153… LOR        5.47e-5 LOR             gtex_v8   #> # ℹ 5 more variables: tissueSiteDetailId <chr>, ontologyId <chr>, #> #   chromosome <chr>, gencodeId <chr>, nes <dbl> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"Find significant single tissue eQTLs using Chromosomal Locations. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, /dataset. default, service queries latest GTEx release. Since endpoint used support third party program portal, return structure different endpoints paginated. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"get_significant_single_tissue_eqtls_by_location(   tissueSiteDetailId,   start,   end,   chromosome,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"# \\dontrun{ get_significant_single_tissue_eqtls_by_location(   tissueSiteDetailId = \"Artery_Aorta\",   start = 10000,   end = 250000,   chromosome = \"chr11\") #> # A tibble: 434 × 11 #>    chromosome datasetId gencodeId      geneSymbol geneSymbolUpper   nes   pValue #>    <chr>      <chr>     <chr>          <chr>      <chr>           <dbl>    <dbl> #>  1 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.381 1.11e- 6 #>  2 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.364 2.25e- 6 #>  3 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.417 3.10e- 8 #>  4 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.480 8.39e- 9 #>  5 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #>  6 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.553 8.89e-10 #>  7 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.577 2.95e-12 #>  8 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.547 6.13e-10 #>  9 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #> 10 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #> # ℹ 424 more rows #> # ℹ 4 more variables: pos <int>, snpId <chr>, tissueSiteDetailId <chr>, #> #   variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"Retrieve Interaction eQTL Data. service returns cell type interaction eQTLs (ieQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"get_significant_single_tissue_ieqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_ieqtls(c(\"ENSG00000132693.12\",                                        \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 86 #> # A tibble: 86 × 24 #>    snpId     bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #>    <chr>     <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>           #>  1 rs34188… 0.0890 1.54e8 RS34188388  0.102  0.00447  LOR        LOR             #>  2 rs24945… 0.0654 1.60e8 RS2494523   0.867  0.00129  CRP        CRP             #>  3 rs986760 0.148  1.53e8 RS986760    0.0454 0.00694  LOR        LOR             #>  4 rs17697… 0.0428 1.59e8 RS17697329  0.515  0.000627 CRP        CRP             #>  5 rs67415… 0.154  1.53e8 RS67415955  0.565  0.000754 LOR        LOR             #>  6 rs12133… 0.157  1.60e8 RS12133356  0.634  0.00106  CRP        CRP             #>  7 rs12132… 0.113  1.53e8 RS12132927  0.858  0.00365  LOR        LOR             #>  8 rs30269… 0.0683 1.59e8 RS3026943   0.684  0.00222  CRP        CRP             #>  9 rs24946… 0.0567 1.54e8 RS2494670   0.516  0.000595 LOR        LOR             #> 10 rs12121… 0.0695 1.60e8 RS12121609  0.444  0.000266 CRP        CRP             #> # ℹ 76 more rows #> # ℹ 16 more variables: pValueI <dbl>, bGI <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, tissueCellType <chr>, #> #   tssDistance <int>, bGSE <dbl>, variantId <chr>, maf <dbl>, bISE <dbl>, #> #   datasetId <chr>, bG <dbl>, pValueAdjustedBH <dbl>, bI <dbl>, #> #   gencodeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"Retrieve Interaction sQTL Data. service retrieves cell type interaction sQTLs (isQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"get_significant_single_tissue_isqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_isqtls(gencodeIds = c(\"ENSG00000065613.9\",                                                     \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 25 #>   snpId      bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #>   <chr>      <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>           #> 1 rs4845790 0.0194 1.53e8 RS4845790  0.00645  8.97e-7 LOR        LOR             #> 2 rs4845790 0.0196 1.53e8 RS4845790  0.0118   1.41e-7 LOR        LOR             #> 3 rs359327… 0.0289 1.54e8 RS35932716 0.0142   3.70e-5 LOR        LOR             #> 4 rs146285… 0.0293 1.53e8 RS1462851… 0.0225   3.03e-5 LOR        LOR             #> # ℹ 17 more variables: pValueI <dbl>, bGI <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, tissueCellType <chr>, #> #   tssDistance <int>, bGSE <dbl>, variantId <chr>, maf <dbl>, bISE <dbl>, #> #   datasetId <chr>, bG <dbl>, pValueAdjustedBH <dbl>, bI <dbl>, #> #   gencodeId <chr>, phenotypeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"Retrieve Single Tissue sQTL Data. service returns single tissue sQTL data given genes, specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"get_significant_single_tissue_sqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_sqtls(gencodeIds = c(\"ENSG00000065613.9\",                                                    \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 176 #> # A tibble: 176 × 14 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs4636462  152442732 RS4636462  chr1_1524… LOR        7.71e-5 LOR             #>  2 rs4845768  152442997 RS4845768  chr1_1524… LOR        6.57e-5 LOR             #>  3 rs12069640 152444300 RS12069640 chr1_1524… LOR        7.13e-5 LOR             #>  4 rs11803629 152445670 RS11803629 chr1_1524… LOR        1.81e-4 LOR             #>  5 rs12125681 152445737 RS12125681 chr1_1524… LOR        1.81e-4 LOR             #>  6 rs11205004 152446586 RS11205004 chr1_1524… LOR        1.81e-4 LOR             #>  7 rs11579085 152447965 RS11579085 chr1_1524… LOR        1.81e-4 LOR             #>  8 rs1885529  152448570 RS1885529  chr1_1524… LOR        1.81e-4 LOR             #>  9 rs1885528  152448978 RS1885528  chr1_1524… LOR        1.81e-4 LOR             #> 10 rs1885527  152449069 RS1885527  chr1_1524… LOR        1.81e-4 LOR             #> # ℹ 166 more rows #> # ℹ 7 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>, #> #   phenotypeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleux Gex — get_single_nucleus_gex","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"Retrieve Single Nucleus Gene Expression Data given Gene. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"get_single_nucleus_gex(   gencodeIds,   datasetId = \"gtex_snrnaseq_pilot\",   tissueSiteDetailIds = NULL,   excludeDataArray = TRUE,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. excludeDataArray String. Options TRUE FALSE page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"# \\dontrun{ # Search for one or more genes - returns a tibble with one row per tissue. # Column \"cellTypes\" now contains a tibble of expression summary data, with # one row for each cell type get_single_nucleus_gex(gencodeIds = c(\"ENSG00000203782.5\",                                       \"ENSG00000132693.12\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 14 #> # A tibble: 14 × 7 #>    tissueSiteDetailId  ontologyId datasetId gencodeId geneSymbol cellTypes unit  #>    <chr>               <chr>      <chr>     <chr>     <chr>      <list>    <chr> #>  1 Muscle_Skeletal     UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  2 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  3 Esophagus_Mucosa    UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  4 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  5 Lung                UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  6 Prostate            UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  7 Skin_Sun_Exposed_L… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  8 Muscle_Skeletal     UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #>  9 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 10 Esophagus_Mucosa    UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 11 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 12 Heart_Left_Ventric… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 13 Lung                UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 14 Prostate            UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(…  # `excludeDataArray = FALSE` - expression values are stored under \"celltypes\" # in an additional column called \"data\" response <- get_single_nucleus_gex(gencodeIds = \"ENSG00000132693.12\",                                    excludeDataArray = FALSE,                                    itemsPerPage = 2) #> Warning: ! Total number of items (7) exceeds maximum page size (2). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 2 #> • totalNumberOfItems = 7  response #> # A tibble: 2 × 7 #>   tissueSiteDetailId   ontologyId datasetId gencodeId geneSymbol cellTypes unit  #>   <chr>                <chr>      <chr>     <chr>     <chr>      <list>    <chr> #> 1 Muscle_Skeletal      UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 2 Breast_Mammary_Tiss… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(…  # \"cellTypes\" contains a tibble of data with one row for each # cell type e.g. for Breast_Mammary_Tissue response$cellTypes[[2]] #> # A tibble: 2 × 8 #>   cellType                  count meanWithZeros meanWithoutZeros medianWithZeros #>   <chr>                     <int>         <dbl>            <dbl>           <dbl> #> 1 Epithelial cell (luminal)     2      0.000902             2.19               0 #> 2 Endothelial cell (vascul…     1      0.00401              3.05               0 #> # ℹ 3 more variables: medianWithoutZeros <dbl>, numZeros <int>, data <list>  # when `excludeDataArray = FALSE`, expression values are stored in \"data\" # e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal): response$cellTypes[[2]]$data[[1]] #> [1] 1.593315 2.782725 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"Retrieve Summarized Single Nucleus Gene Expression Data. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"get_single_nucleus_gex_summary(   datasetId = \"gtex_snrnaseq_pilot\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"# \\dontrun{ # all tissues get_single_nucleus_gex_summary() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 114 #> # A tibble: 114 × 5 #>    tissueSiteDetailId ontologyId     datasetId           cellType       numCells #>    <chr>              <chr>          <chr>               <chr>             <int> #>  1 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …      769 #>  2 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (NMJ-…       95 #>  3 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Endothelial c…     1124 #>  4 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …    20772 #>  5 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Fibroblast         5944 #>  6 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Pericyte/SMC        448 #>  7 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Immune (DC/ma…      721 #>  8 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Adipocyte           159 #>  9 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Schwann cell         35 #> 10 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Satellite cell      487 #> # ℹ 104 more rows  # filter for specific tissue get_single_nucleus_gex_summary(tissueSiteDetailIds = c(\"Breast_Mammary_Tissue\",                                                        \"Skin_Sun_Exposed_Lower_leg\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25 #> # A tibble: 25 × 5 #>    tissueSiteDetailId         ontologyId     datasetId         cellType numCells #>    <chr>                      <chr>          <chr>             <chr>       <int> #>  1 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Epithel…     4849 #>  2 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Adipocy…     1761 #>  3 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Immune …      358 #>  4 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Myoepit…      950 #>  5 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Fibrobl…      819 #>  6 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      762 #>  7 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      119 #>  8 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Pericyt…      152 #>  9 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Sweat g…      300 #> 10 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Epithel…       72 #> # ℹ 15 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sqtl Genes — get_sqtl_genes","title":"Get Sqtl Genes — get_sqtl_genes","text":"Retrieve sGenes (sQTL Genes). service returns sGenes (sQTL Genes) specified dataset. Results may filtered tissue. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"get_sqtl_genes(   tissueSiteDetailId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sqtl Genes — get_sqtl_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sqtl Genes — get_sqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"# \\dontrun{ get_sqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (3013) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 13 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3013 #> # A tibble: 250 × 11 #>    nPhenotypes pValueThreshold phenotypeId        geneSymbol    pValue datasetId #>          <int>           <dbl> <chr>              <chr>          <dbl> <chr>     #>  1           9      0.0000145  chr1:15947:16607:… WASH7P     7.15e-  8 gtex_v8   #>  2           6      0.00000634 chr1:1090428:1091… C1orf159   6.85e- 10 gtex_v8   #>  3           7      0.00000908 chr1:1228946:1231… SDF4       1.16e-188 gtex_v8   #>  4           6      0.00000861 chr1:1310688:1310… PUSL1      2.50e- 40 gtex_v8   #>  5           3      0.00000954 chr1:1325102:1327… CPTP       9.60e-  7 gtex_v8   #>  6           2      0.0000147  chr1:1487914:1489… ATAD3C     1.61e- 25 gtex_v8   #>  7           5      0.00000740 chr1:1487914:1489… ATAD3B     1.61e- 25 gtex_v8   #>  8           2      0.0000361  chr1:1545002:1547… SSU72      3.28e- 25 gtex_v8   #>  9          19      0.00000176 chr1:1629311:1629… MIB2       1.97e- 12 gtex_v8   #> 10           8      0.00000273 chr1:1641113:1641… CDK11B     3.08e- 56 gtex_v8   #> # ℹ 240 more rows #> # ℹ 5 more variables: empiricalPValue <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, qValue <dbl>, gencodeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Subject — get_subject","title":"Get Subject — get_subject","text":"service returns information subjects used analyses datasets. Results may filtered dataset ID, subject ID, sex, age bracket Hardy Scale. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Subject — get_subject","text":"","code":"get_subject(   datasetId = \"gtex_v8\",   sex = NULL,   ageBrackets = NULL,   hardyScales = NULL,   subjectIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Subject — get_subject","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sex String. Options: \"male\", \"female\". ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". subjectIds Character vector. GTEx subject ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Subject — get_subject","text":"Tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Subject — get_subject","text":"","code":"# \\dontrun{   get_subject() #> Warning: ! Total number of items (979) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 979 #> # A tibble: 250 × 5 #>    hardyScale                  ageBracket subjectId  sex    datasetId #>    <chr>                       <chr>      <chr>      <chr>  <chr>     #>  1 Slow death                  60-69      GTEX-1117F female gtex_v8   #>  2 Ventilator case             50-59      GTEX-111CU male   gtex_v8   #>  3 Fast death - violent        60-69      GTEX-111FC male   gtex_v8   #>  4 Intermediate death          60-69      GTEX-111VG male   gtex_v8   #>  5 Ventilator case             60-69      GTEX-111YS male   gtex_v8   #>  6 Ventilator case             60-69      GTEX-1122O female gtex_v8   #>  7 Fast death - natural causes 60-69      GTEX-1128S female gtex_v8   #>  8 NA                          60-69      GTEX-113IC male   gtex_v8   #>  9 Fast death - natural causes 50-59      GTEX-113JC female gtex_v8   #> 10 Fast death - natural causes 60-69      GTEX-117XS male   gtex_v8   #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Tissue Site Detail — get_tissue_site_detail","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"Retrieve tissue site detail information database GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"get_tissue_site_detail(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"# \\dontrun{   # returns a tibble with one row per tissue   get_tissue_site_detail() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 18 #>    tissueSiteDetailId  colorHex colorRgb datasetId eGeneCount expressedGeneCount #>    <chr>               <chr>    <chr>    <chr>          <int>              <int> #>  1 Adipose_Subcutaneo… FF6600   255,102… gtex_v8        15607              28830 #>  2 Adipose_Visceral_O… FFAA00   255,170… gtex_v8        12482              28881 #>  3 Adrenal_Gland       33DD33   51,221,… gtex_v8         8123              28235 #>  4 Artery_Aorta        FF5555   255,85,… gtex_v8        12493              28025 #>  5 Artery_Coronary     FFAA99   255,170… gtex_v8         6296              28462 #>  6 Artery_Tibial       FF0000   255,0,0  gtex_v8        15008              27217 #>  7 Bladder             AA0000   170,0,0  gtex_v8           NA              28949 #>  8 Brain_Amygdala      EEEE00   238,238… gtex_v8         3726              28196 #>  9 Brain_Anterior_cin… EEEE00   238,238… gtex_v8         5640              28921 #> 10 Brain_Caudate_basa… EEEE00   238,238… gtex_v8         8362              29230 #> # ℹ 44 more rows #> # ℹ 12 more variables: hasEGenes <lgl>, hasSGenes <lgl>, mappedInHubmap <lgl>, #> #   eqtlSampleSummary <list>, rnaSeqSampleSummary <list>, sGeneCount <int>, #> #   samplingSite <chr>, tissueSite <chr>, tissueSiteDetail <chr>, #> #   tissueSiteDetailAbbr <chr>, ontologyId <chr>, ontologyIri <chr>    # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns   bladder_site_details <- get_tissue_site_detail() |>     dplyr::filter(tissueSiteDetailId == \"Bladder\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54    purrr::pluck(bladder_site_details, \"eqtlSampleSummary\", 1) #> $totalCount #> [1] 21 #>  #> $female #> $female$ageMax #> [1] 59 #>  #> $female$ageMin #> [1] 27 #>  #> $female$ageMean #> [1] 43.6 #>  #> $female$count #> [1] 7 #>  #>  #> $male #> $male$ageMax #> [1] 61 #>  #> $male$ageMin #> [1] 21 #>  #> $male$ageMean #> [1] 46 #>  #> $male$count #> [1] 14 #>  #>     purrr::pluck(bladder_site_details, \"rnaSeqSampleSummary\", 1) #> $totalCount #> [1] 21 #>  #> $female #> $female$ageMax #> [1] 59 #>  #> $female$ageMin #> [1] 27 #>  #> $female$ageMean #> [1] 43.6 #>  #> $female$count #> [1] 7 #>  #>  #> $male #> $male$ageMax #> [1] 61 #>  #> $male$ageMin #> [1] 21 #>  #> $male$ageMean #> [1] 46 #>  #> $male$count #> [1] 14 #>  #>  # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Top Expressed Genes — get_top_expressed_genes","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"Find top expressed genes specified tissue. Returns top expressed genes specified tissue dataset, sorted median expression. optional parameter filterMtGene set true, mitochondrial genes excluded results. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"get_top_expressed_genes(   tissueSiteDetailId,   datasetId = \"gtex_v8\",   filterMtGene = TRUE,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". filterMtGene Logical. Exclude mitochondrial genes. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"# \\dontrun{ get_top_expressed_genes(tissueSiteDetailId = \"Artery_Aorta\") #> Warning: ! Total number of items (56163) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 225 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 56163 #> # A tibble: 250 × 7 #>    tissueSiteDetailId ontologyId     datasetId gencodeId geneSymbol median unit  #>    <chr>              <chr>          <chr>     <chr>     <chr>       <dbl> <chr> #>  1 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MGP        11936. TPM   #>  2 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FTL         9196. TPM   #>  3 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTB        9154. TPM   #>  4 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… BGN         8167. TPM   #>  5 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… TAGLN       6099. TPM   #>  6 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTA2       5736. TPM   #>  7 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… IGFBP7      5639. TPM   #>  8 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MYL9        4275. TPM   #>  9 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… HSPB1       3780. TPM   #> 10 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FLNA        3732. TPM   #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Transcripts — get_transcripts","title":"Get Transcripts — get_transcripts","text":"Find transcripts reference gene. service returns information transcripts given versioned GENCODE ID. genome build GENCODE version must provided. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Transcripts — get_transcripts","text":"","code":"get_transcripts(   gencodeId,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Transcripts — get_transcripts","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Transcripts — get_transcripts","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Transcripts — get_transcripts","text":"","code":"# \\dontrun{ get_transcripts(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 11 #>    start    end featureType genomeBuild transcriptId source chromosome gencodeId #>    <int>  <int> <chr>       <chr>       <chr>        <chr>  <chr>      <chr>     #> 1 1.53e8 1.53e8 transcript  GRCh38/hg38 ENST0000036… HAVANA chr1       ENSG0000… #> # ℹ 3 more variables: geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant — get_variant","title":"Get Variant — get_variant","text":"service returns information variant, including position, dbSNP RS ID, reference allele, alternative allele, whether minor allele frequency >= 1%. GTEx v6p, also information whether whole exome sequence chip sequencing data available. Results may queried GTEx variant ID (variantId), dbSNP RS ID (snpId) genomic location (chromosome pos). Variants identified based genotype data dataset cohort, namely, dataset-dependent. variant assigned unique GTEx variant ID (.e. primary key). variants mappable dbSNP RS ID. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant — get_variant","text":"","code":"get_variant(   snpId = NULL,   variantId = NULL,   chromosome = NULL,   pos = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant — get_variant","text":"snpId String variantId String. gtex variant ID. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". pos Integer, vector. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant — get_variant","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant — get_variant","text":"","code":"# search by rsid get_variant(snpId = \"rs1410858\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #>   snpId     b37VariantId         pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>     <chr>              <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> # ℹ 2 more variables: datasetId <chr>, ref <chr>  # search by variantId get_variant(variantId = \"chr1_153209640_C_A_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #>   snpId     b37VariantId         pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>     <chr>              <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> # ℹ 2 more variables: datasetId <chr>, ref <chr>  # search by chromosome and position get_variant(chromosome = \"chr1\",             pos = 153209600:153209700) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #>   snpId       b37VariantId       pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>       <chr>            <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs11205220  1_153182115_T_… 1.53e8 TRUE  chr1_153… C     chr1       RS11205220 #> 2 rs1410858   1_153182116_C_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T     chr1       RS1392967… #> 4 rs80104092  1_153182149_T_… 1.53e8 FALSE chr1_153… C     chr1       RS80104092 #> # ℹ 2 more variables: datasetId <chr>, ref <chr>"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant By Location — get_variant_by_location","title":"Get Variant By Location — get_variant_by_location","text":"service allows user query information variants certain chromosome certain location. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(   start,   end,   chromosome,   sortBy = \"pos\",   sortDirection = \"asc\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant By Location — get_variant_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant By Location — get_variant_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(start = 153209600,                         end = 153209700,                         chromosome = \"chr1\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #>   snpId       b37VariantId       pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>       <chr>            <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs11205220  1_153182115_T_… 1.53e8 TRUE  chr1_153… C     chr1       RS11205220 #> 2 rs1410858   1_153182116_C_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T     chr1       RS1392967… #> 4 rs80104092  1_153182149_T_… 1.53e8 FALSE chr1_153… C     chr1       RS80104092 #> # ℹ 2 more variables: datasetId <chr>, ref <chr>"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr: Query the GTEx Portal API — gtexr-package","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"convenient R interface Genotype-Tissue Expression (GTEx) Portal API. information API, see https://gtexportal.org/api/v2/redoc.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"Maintainer: Alasdair Warwick alasdair.warwick.19@ucl.ac.uk (ORCID) [copyright holder] Authors: Benjamin Zuckerman (ORCID) Abraham Olvera-Barrios (ORCID) Chuin Ying Ung (ORCID) Robert Luben (ORCID)","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr arguments — gtexr_arguments","title":"gtexr arguments — gtexr_arguments","text":"Internal function documents arguments exported gtexr functions wrap GTEx Portal API endpoints (using roxygen @inheritParams tag).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gtexr arguments — gtexr_arguments","text":"","code":"gtexr_arguments(   ageBrackets = NULL,   aliquotIds = NULL,   attributeSubset = NULL,   autolysisScores = NULL,   cellType = NULL,   bp_window = NULL,   chromosome = NULL,   datasetId = NULL,   dataTypes = NULL,   draw = NULL,   end = NULL,   excludeDataArray = NULL,   .featureId = NULL,   filterMtGene = NULL,   gencodeId = NULL,   gencodeIds = NULL,   gencodeVersion = NULL,   geneId = NULL,   geneIds = NULL,   genomeBuild = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL,   itemsPerPage = NULL,   ischemicTime = NULL,   ischemicTimeGroups = NULL,   materialTypes = NULL,   organizationName = NULL,   page = NULL,   pathCategory = NULL,   phenotypeId = NULL,   pos = NULL,   project_id = NULL,   rin = NULL,   sampleId = NULL,   sampleIds = NULL,   searchTerm = NULL,   sex = NULL,   snpId = NULL,   sortBy = NULL,   sortDirection = NULL,   start = NULL,   subjectIds = NULL,   tissueSampleIds = NULL,   tissueSiteDetailId = NULL,   tissueSiteDetailIds = NULL,   uberonIds = NULL,   variantId = NULL,   variantIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gtexr arguments — gtexr_arguments","text":"ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". aliquotIds Character vector. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". bp_window Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". draw Integer. end Integer. excludeDataArray String. Options TRUE FALSE .featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. filterMtGene Logical. Exclude mitochondrial genes. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". geneId String. gene symbol, gencode ID, Ensemble ID. geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. itemsPerPage Integer (default = 250). ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\". page Integer (default = 0). pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". phenotypeId String. See GTEx portal FAQs details. pos Integer, vector. project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\". rin Integer vector. sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ sampleIds Character vector. GTEx sample ID. searchTerm String. sex String. Options: \"male\", \"female\". snpId String sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". start Integer. subjectIds Character vector. GTEx subject ID. tissueSampleIds Array strings. list Tissue Sample ID(s). tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). variantId String. gtex variant ID. variantIds Character vector. Gtex variant IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gtexr arguments — gtexr_arguments","text":"Returns NULL invisibly. Used documentation .","code":""},{"path":"https://rmgpanw.github.io/gtexr/news/index.html","id":"gtexr-development-version","dir":"Changelog","previous_headings":"","what":"gtexr (development version)","title":"gtexr (development version)","text":"Initial CRAN submission.","code":""}]
+[{"path":"https://rmgpanw.github.io/gtexr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 gtexr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/developer_guide.html","id":"functions","dir":"Articles","previous_headings":"","what":"Functions","title":"Developer guide","text":"Function name title API endpoint lower case, words separated underscores. @description section copied verbatim API documentation site ends link corresponding API endpoint documentation. notes may added @details. Names match API endpoint, except argument accepts array (vector R) values, case pluralised.1 Default values also match API endpoint. Query parameters flagged “required” GTEx Portal API documentation default values.2 documented gtexr_arguments.R. functions therefore use @inheritParams gtexr_arguments documentation. Use @family roxygen tag match categories API documentation. used categorise functions pkgdown site reference page. Return tibble. first example @examples must produce output single function call without assignment (e.g. get_news_items(), x <- get_news_items()). used pre-populate argument values gtexr shiny app working example. examples surrounded \\dontrun{}.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"shiny-app","dir":"Articles","previous_headings":"","what":"Shiny app","title":"Introduction to gtexr","text":"Users can try functions interatively ⭐gtexr shiny app⭐, pre-populates query parameters first working example function’s documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"Introduction to gtexr","text":"rest vignette outlines example applications gtexr.","code":"library(gtexr) library(dplyr) library(purrr)"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-build-37-coordinates-for-a-variant","dir":"Articles","previous_headings":"Examples","what":"Get build 37 coordinates for a variant","title":"Introduction to gtexr","text":"","code":"get_variant(snpId = \"rs1410858\") |>   tidyr::separate(     col = b37VariantId,     into = c(       \"chromosome\",       \"position\",       \"reference_allele\",       \"alternative_allele\",       \"genome_build\"     ),     sep = \"_\",     remove = FALSE   ) |>   select(snpId:genome_build) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #>   snpId     b37VariantId chromosome position reference_allele alternative_allele #>   <chr>     <chr>        <chr>      <chr>    <chr>            <chr>              #> 1 rs1410858 1_153182116… 1          1531821… C                A                  #> # ℹ 1 more variable: genome_build <chr>"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-gene-symbol-to-versioned-gencode-id","dir":"Articles","previous_headings":"Examples","what":"Convert gene symbol to versioned GENCODE ID","title":"Introduction to gtexr","text":"Use get_gene() get_genes()","code":"get_genes(\"CRP\") |>   select(geneSymbol, gencodeId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #>   geneSymbol gencodeId          #>   <chr>      <chr>              #> 1 CRP        ENSG00000132693.12"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-rsid-to-gtex-variant-id","dir":"Articles","previous_headings":"Examples","what":"Convert rsID to GTEx variant ID","title":"Introduction to gtexr","text":"Use get_variant()","code":"get_variant(snpId = \"rs1410858\") |>   select(snpId, variantId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #>   snpId     variantId              #>   <chr>     <chr>                  #> 1 rs1410858 chr1_153209640_C_A_b38"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"for-a-gene-of-interest-which-tissues-have-significant-cis-eqtls","dir":"Articles","previous_headings":"Examples","what":"For a gene of interest, which tissues have significant cis-eQTLs?","title":"Introduction to gtexr","text":"Use get_significant_single_tissue_eqtls() (note requires versioned GENCODE IDs)","code":"gene_symbol_of_interest <- \"CRP\"  gene_gencodeId_of_interest <- get_genes(gene_symbol_of_interest) |>   pull(gencodeId) |>   suppressMessages()  gene_gencodeId_of_interest |>   get_significant_single_tissue_eqtls() |>   distinct(geneSymbol, gencodeId, tissueSiteDetailId) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 93 #> # A tibble: 3 × 3 #>   geneSymbol gencodeId          tissueSiteDetailId                  #>   <chr>      <chr>              <chr>                               #> 1 CRP        ENSG00000132693.12 Thyroid                             #> 2 CRP        ENSG00000132693.12 Esophagus_Gastroesophageal_Junction #> 3 CRP        ENSG00000132693.12 Muscle_Skeletal"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-data-for-non-eqtl-variants","dir":"Articles","previous_headings":"Examples","what":"Get data for non-eQTL variants","title":"Introduction to gtexr","text":"analyses (e.g. Mendelian randomisation) require data variants may may significant eQTLs. Use calculate_expression_quantitative_trait_loci() purrr::map() retrieve data multiple variants","code":"variants_of_interest <- c(\"rs12119111\", \"rs6605071\", \"rs1053870\")  variants_of_interest |>   set_names() |>   map(     \\(x) calculate_expression_quantitative_trait_loci(       tissueSiteDetailId = \"Liver\",       gencodeId = \"ENSG00000237973.1\",       variantId = x     )   ) |>   bind_rows(.id = \"rsid\") |>      # optionally, reformat output - first extract genomic coordinates and alleles   tidyr::separate(     col = \"variantId\",     into = c(       \"chromosome\",       \"position\",       \"reference_allele\",       \"alternative_allele\",       \"genome_build\"     ),     sep = \"_\"   ) |>      # ...then ascertain alternative_allele frequency   mutate(     alt_allele_count = (2 * homoAltCount) + hetCount,     total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),     alternative_allele_frequency = alt_allele_count / total_allele_count   ) |>      select(     rsid,     beta = nes,     se = error,     pValue,     minor_allele_frequency = maf,     alternative_allele_frequency,     chromosome:genome_build,     tissueSiteDetailId   ) #> # A tibble: 3 × 12 #>   rsid         beta     se  pValue minor_allele_frequency alternative_allele_f…¹ #>   <chr>       <dbl>  <dbl>   <dbl>                  <dbl>                  <dbl> #> 1 rs121191…  0.0270 0.0670 6.88e-1                 0.365                   0.635 #> 2 rs6605071 -0.601  0.166  3.88e-4                 0.0409                  0.959 #> 3 rs1053870  0.0247 0.0738 7.38e-1                 0.214                   0.214 #> # ℹ abbreviated name: ¹​alternative_allele_frequency #> # ℹ 6 more variables: chromosome <chr>, position <chr>, reference_allele <chr>, #> #   alternative_allele <chr>, genome_build <chr>, tissueSiteDetailId <chr>"},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alasdair Warwick. Author, maintainer, copyright holder. Benjamin Zuckerman. Author. Abraham Olvera-Barrios. Author. Chuin Ying Ung. Author. Robert Luben. Author.","code":""},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Warwick , Zuckerman B, Olvera-Barrios , Ung C, Luben R (2024). gtexr: Query GTEx Portal API. R package version 0.1.0, https://github.com/rmgpanw/gtexr, https://rmgpanw.github.io/gtexr/.","code":"@Manual{,   title = {gtexr: Query the GTEx Portal API},   author = {Alasdair Warwick and Benjamin Zuckerman and Abraham Olvera-Barrios and Chuin Ying Ung and Robert Luben},   year = {2024},   note = {R package version 0.1.0,     https://github.com/rmgpanw/gtexr},   url = {https://rmgpanw.github.io/gtexr/}, }"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"gtexr-","dir":"","previous_headings":"","what":"Query the GTEx Portal API","title":"Query the GTEx Portal API","text":"goal gtexr provide convenient R interface GTEx Portal API V2. New R? Try ⭐shiny app⭐.","code":""},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Query the GTEx Portal API","text":"can install package CRAN: can install development version gtexr GitHub :","code":"install.packages(\"gtexr\") # install.packages(\"devtools\") devtools::install_github(\"rmgpanw/gtexr\")"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Query the GTEx Portal API","text":"Get general information GTEx service: Retrieve eQTL genes whole blood tissue: Retrieve significant eQTLs one genes:","code":"library(gtexr) get_service_info() #> # A tibble: 1 × 9 #>   id     name  version organization_name organization_url description contactUrl #>   <chr>  <chr> <chr>   <chr>             <chr>            <chr>       <chr>      #> 1 org.g… GTEx… 2.0.0   GTEx Project      https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl <chr>, environment <chr> get_eqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (12360) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 50 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 12360 #> # A tibble: 250 × 10 #>    tissueSiteDetailId ontologyId  datasetId empiricalPValue gencodeId geneSymbol #>    <chr>              <chr>       <chr>               <dbl> <chr>     <chr>      #>  1 Whole_Blood        UBERON:001… gtex_v8          1.05e- 9 ENSG0000… WASH7P     #>  2 Whole_Blood        UBERON:001… gtex_v8          1.06e-25 ENSG0000… RP11-34P1… #>  3 Whole_Blood        UBERON:001… gtex_v8          6.31e- 2 ENSG0000… CICP27     #>  4 Whole_Blood        UBERON:001… gtex_v8          8.71e- 9 ENSG0000… RP11-34P1… #>  5 Whole_Blood        UBERON:001… gtex_v8          6.01e-20 ENSG0000… RP11-34P1… #>  6 Whole_Blood        UBERON:001… gtex_v8          6.96e- 9 ENSG0000… RP11-34P1… #>  7 Whole_Blood        UBERON:001… gtex_v8          3.10e- 4 ENSG0000… RP11-34P1… #>  8 Whole_Blood        UBERON:001… gtex_v8          1.92e- 3 ENSG0000… ABC7-4304… #>  9 Whole_Blood        UBERON:001… gtex_v8          1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood        UBERON:001… gtex_v8          7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, qValue <dbl> get_significant_single_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs12128960 159343657 RS12128960 chr1_1593… CRP        8.52e-5 CRP             #>  2 rs12132451 159344052 RS12132451 chr1_1593… CRP        7.92e-5 CRP             #>  3 rs12136402 159347493 RS12136402 chr1_1593… CRP        7.92e-5 CRP             #>  4 rs10908709 159350390 RS10908709 chr1_1593… CRP        7.92e-5 CRP             #>  5 rs10908710 159351189 RS10908710 chr1_1593… CRP        7.92e-5 CRP             #>  6 rs11265178 159359256 RS11265178 chr1_1593… CRP        9.62e-5 CRP             #>  7 rs35532309 159360755 RS35532309 chr1_1593… CRP        6.11e-5 CRP             #>  8 rs6692378  159369451 RS6692378  chr1_1593… CRP        1.17e-6 CRP             #>  9 rs10908714 159370563 RS10908714 chr1_1593… CRP        1.80e-5 CRP             #> 10 rs6656924  159372915 RS6656924  chr1_1593… CRP        1.00e-6 CRP             #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Calculate eQTLs service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"calculate_expression_quantitative_trait_loci(   tissueSiteDetailId,   gencodeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Notes output: Beta standard error recorded columns nes error respectively (see GTEx FAQs) variantId contains (order) chromosome, position, reference allele, alternative allele human genome build separated underscores. reference alternative alleles \"chr1_13550_G_A_b38\" example \"G\" \"\" respectively. See examples calculate minor alternative allele frequencies. Notes input: Argument variantId also accepts RSIDs.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\",                                              gencodeId = \"ENSG00000203782.5\",                                              variantId = \"rs79641866\") #> # A tibble: 1 × 15 #>   data               error gencodeId  geneSymbol genotypes hetCount homoAltCount #>   <list>             <dbl> <chr>      <chr>      <list>       <int>        <int> #> 1 <tibble [670 × 1]> 0.148 ENSG00000… LOR        <tibble>        38            0 #> # ℹ 8 more variables: homoRefCount <int>, maf <dbl>, nes <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, tStatistic <dbl>, tissueSiteDetailId <chr>, #> #   variantId <chr>  # unnest list columns with tidyr::unnest() calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\",                                              gencodeId = \"ENSG00000203782.5\",                                              variantId = \"rs79641866\") |>   tidyr::unnest(c(\"data\", \"genotypes\")) #> # A tibble: 670 × 15 #>      data error gencodeId         geneSymbol genotypes hetCount homoAltCount #>     <dbl> <dbl> <chr>             <chr>          <int>    <int>        <int> #>  1  0.949 0.148 ENSG00000203782.5 LOR                0       38            0 #>  2  1.86  0.148 ENSG00000203782.5 LOR                0       38            0 #>  3 -0.641 0.148 ENSG00000203782.5 LOR                0       38            0 #>  4  0.683 0.148 ENSG00000203782.5 LOR                0       38            0 #>  5 -0.321 0.148 ENSG00000203782.5 LOR                0       38            0 #>  6  0.539 0.148 ENSG00000203782.5 LOR                0       38            0 #>  7  0.266 0.148 ENSG00000203782.5 LOR                0       38            0 #>  8 -1.10  0.148 ENSG00000203782.5 LOR                0       38            0 #>  9 -1.88  0.148 ENSG00000203782.5 LOR                0       38            0 #> 10 -1.03  0.148 ENSG00000203782.5 LOR                0       38            0 #> # ℹ 660 more rows #> # ℹ 8 more variables: homoRefCount <int>, maf <dbl>, nes <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, tStatistic <dbl>, tissueSiteDetailId <chr>, #> #   variantId <chr>  # to calculate minor and alternative allele frequencies calculate_expression_quantitative_trait_loci(   tissueSiteDetailId = \"Liver\",   gencodeId = \"ENSG00000237973.1\",   variantId = \"rs12119111\" ) |>  dplyr::bind_rows(.id = \"rsid\") |>   tidyr::separate(    col = \"variantId\",    into = c(      \"chromosome\",      \"position\",      \"reference_allele\",      \"alternative_allele\",      \"genome_build\"    ),    sep = \"_\"  ) |>   # ...then ascertain alternative_allele frequency  dplyr::mutate(    alt_allele_count = (2 * homoAltCount) + hetCount,    total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),    alternative_allele_frequency = alt_allele_count / total_allele_count  ) |>   dplyr::select(    rsid,    beta = nes,    se = error,    pValue,    minor_allele_frequency = maf,    alternative_allele_frequency,    chromosome:genome_build,    tissueSiteDetailId  ) #> # A tibble: 1 × 12 #>   rsid    beta     se pValue minor_allele_frequency alternative_allele_frequency #>   <chr>  <dbl>  <dbl>  <dbl>                  <dbl>                        <dbl> #> 1 1     0.0270 0.0670  0.688                  0.365                        0.635 #> # ℹ 6 more variables: chromosome <chr>, position <chr>, reference_allele <chr>, #> #   alternative_allele <chr>, genome_build <chr>, tissueSiteDetailId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Ieqtls — calculate_ieqtls","title":"Calculate Ieqtls — calculate_ieqtls","text":"Calculate Cell Specific eQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"calculate_ieqtls(   cellType,   tissueSiteDetailId,   gencodeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Ieqtls — calculate_ieqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Ieqtls — calculate_ieqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"# \\dontrun{ # perform request calculate_ieqtls(cellType = \"Adipocytes\",                  tissueSiteDetailId = \"Adipose_Subcutaneous\",                  gencodeId = \"ENSG00000203782.5\",                  variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #>   cellType  data  datasetId enrichmentScores gencodeId genotypes regressionCoord #>   <chr>     <lis> <chr>     <list>           <chr>     <list>    <list>          #> 1 Adipocyt… <dbl> gtex_v8   <dbl [581]>      ENSG0000… <int>     <named list>    #> # ℹ 2 more variables: tissueSiteDetailId <chr>, variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Isqtls — calculate_isqtls","title":"Calculate Isqtls — calculate_isqtls","text":"Calculate Cell Specific sQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"calculate_isqtls(   cellType,   tissueSiteDetailId,   phenotypeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Isqtls — calculate_isqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Isqtls — calculate_isqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"# \\dontrun{ # perform request calculate_isqtls(cellType = \"Neutrophils\",                  tissueSiteDetailId = \"Whole_Blood\",                  phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\",                  variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #>   cellType    data   datasetId enrichmentScores phenotypeId   tissueSiteDetailId #>   <chr>       <list> <chr>     <list>           <chr>         <chr>              #> 1 Neutrophils <dbl>  gtex_v8   <dbl [670]>      chr1:15947:1… Whole_Blood        #> # ℹ 3 more variables: variantId <chr>, genotypes <list>, regressionCoord <list> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"calculate_splicing_quantitative_trait_loci(   tissueSiteDetailId,   phenotypeId,   variantId,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_splicing_quantitative_trait_loci(   tissueSiteDetailId = \"Whole_Blood\",   phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\",   variantId = \"chr1_14677_G_A_b38\") #> # A tibble: 1 × 14 #>   data     error genotypes hetCount homoAltCount homoRefCount    maf   nes #>   <list>   <dbl> <list>       <int>        <int>        <int>  <dbl> <dbl> #> 1 <tibble> 0.139 <tibble>        69            0          601 0.0515 0.757 #> # ℹ 6 more variables: pValue <dbl>, pValueThreshold <dbl>, phenotypeId <chr>, #> #   tStatistic <dbl>, tissueSiteDetailId <chr>, variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download — download","title":"Download — download","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download — download","text":"","code":"download(   materialTypes = NULL,   tissueSiteDetailIds = NULL,   pathCategory = NULL,   tissueSampleIds = NULL,   sex = NULL,   sortBy = NULL,   sortDirection = NULL,   searchTerm = NULL,   sampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download — download","text":"materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download — download","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download — download","text":"Note: running request filters (.e. download()) raises error.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download — download","text":"","code":"# \\dontrun{ download(   materialTypes = \"RNA:Total RNA\",   tissueSiteDetailIds = \"Thyroid\",   pathCategory = \"clean_specimens\",   sex = \"male\",   ageBrackets = \"50-59\" ) #> # A tibble: 1 × 26 #>   materialType  sampleId    sampleIdUpper sex     rin hasGTExImage concentration #>   <chr>         <chr>       <chr>         <chr> <dbl> <lgl>                <dbl> #> 1 RNA:Total RNA GTEX-WYJK-… GTEX-WYJK-16… male   7.28 TRUE                  36.4 #> # ℹ 19 more variables: analysisRelease <chr>, genotype <chr>, hardyScale <chr>, #> #   pathologyNotes <chr>, subjectId <chr>, tissueSiteDetailId <chr>, #> #   hasGenotype <lgl>, originalMaterialType <chr>, aliquotId <chr>, #> #   tissueSampleId <chr>, ageBracket <chr>, brainTissueDonor <lgl>, #> #   volume <dbl>, hasExpressionData <lgl>, hasBRDImage <lgl>, #> #   tissueSiteDetail <chr>, pathologyNotesCategories <tibble[,57]>, #> #   amount <dbl>, tissueSite <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotation — get_annotation","title":"Get Annotation — get_annotation","text":"service returns list annotations allowed values particular dataset can subsetted. Results may filtered dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotation — get_annotation","text":"","code":"get_annotation(datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotation — get_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotation — get_annotation","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Annotation — get_annotation","text":"Note: output function appears incomplete currently.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotation — get_annotation","text":"","code":"# \\dontrun{  get_annotation() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 5 #>   entity  values    type  annotation datasetId #>   <chr>   <list>    <chr> <chr>      <chr>     #> 1 subject <chr [2]> enum  sex        gtex_v8   #> 2 subject <chr [6]> enum  ageBracket gtex_v8   # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"Find median transcript expression data along hierarchical clusters. Returns median normalized transcript expression tissues known transcripts given gene along hierarchical clustering results tissues transcripts, based exon expression, Newick format. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"get_clustered_median_exon_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"# \\dontrun{ get_clustered_median_exon_expression(c(\"ENSG00000203782.5\",                                        \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 216 × 8 #>     median exonId   tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #>      <dbl> <chr>    <chr>              <chr>      <chr>     <chr>     <chr>      #>  1  0.789  ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… CRP        #>  2 16.8    ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… CRP        #>  3  0.0921 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… CRP        #>  4 12      ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… CRP        #>  5  1      ENSG000… Adrenal_Gland      UBERON:00… gtex_v8   ENSG0000… CRP        #>  6 22.7    ENSG000… Adrenal_Gland      UBERON:00… gtex_v8   ENSG0000… CRP        #>  7  0      ENSG000… Artery_Aorta       UBERON:00… gtex_v8   ENSG0000… CRP        #>  8  8      ENSG000… Artery_Aorta       UBERON:00… gtex_v8   ENSG0000… CRP        #>  9  0      ENSG000… Artery_Coronary    UBERON:00… gtex_v8   ENSG0000… CRP        #> 10 14      ENSG000… Artery_Coronary    UBERON:00… gtex_v8   ENSG0000… CRP        #> # ℹ 206 more rows #> # ℹ 1 more variable: unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_exon_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $exon #> [1] \"((ENSG00000203782.5_2:8.51,ENSG00000132693.12_2:8.51):0.79,(ENSG00000203782.5_1:5.92,ENSG00000132693.12_1:5.92):3.38);\" #>  #> $tissue #> [1] \"(((((((((((Uterus:0.02,Stomach:0.02):0.04,(Pituitary:0.02,Brain_Cerebellum:0.02):0.04):0.01,((((Thyroid:0.03,Colon_Transverse:0.03):0.00,((Artery_Coronary:0.02,Adipose_Visceral_Omentum:0.02):0.00,(Esophagus_Muscularis:0.01,Esophagus_Gastroesophageal_Junction:0.01):0.01):0.01):0.01,Small_Intestine_Terminal_Ileum:0.04):0.00,Artery_Aorta:0.04):0.03):0.04,Kidney_Cortex:0.11):0.00,Brain_Cerebellar_Hemisphere:0.11):0.02,(((((((Ovary:0.01,Nerve_Tibial:0.01):0.00,Adipose_Subcutaneous:0.01):0.01,Esophagus_Mucosa:0.02):0.01,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.02):0.01,Minor_Salivary_Gland:0.03):0.01,(Prostate:0.02,Lung:0.02):0.02):0.04,Testis:0.09):0.04):0.02,((Fallopian_Tube:0.09,Cervix_Ectocervix:0.09):0.01,((Kidney_Medulla:0.06,Bladder:0.06):0.03,((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.04,Cervix_Endocervix:0.05):0.03):0.02):0.05):0.03,((Vagina:0.09,Brain_Hypothalamus:0.09):0.03,((((((Brain_Hippocampus:0.01,Brain_Amygdala:0.01):0.01,Cells_EBV-transformed_lymphocytes:0.02):0.01,Brain_Frontal_Cortex_BA9:0.02):0.01,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.03):0.02,(Brain_Cortex:0.02,Brain_Anterior_cingulate_cortex_BA24:0.02):0.03):0.02,(((((Brain_Substantia_nigra:0.01,Artery_Tibial:0.01):0.00,(Heart_Atrial_Appendage:0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00):0.00,Muscle_Skeletal:0.01):0.01,Colon_Sigmoid:0.02):0.01,(Whole_Blood:0.02,Heart_Left_Ventricle:0.02):0.02):0.04):0.05):0.06):0.20,Pancreas:0.39):0.34,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.71):0.12,Liver:0.85);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues along hierarchical clustering results tissues genes, based gene expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"get_clustered_median_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"# \\dontrun{ get_clustered_median_gene_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 108 × 7 #>    median tissueSiteDetailId     ontologyId datasetId gencodeId geneSymbol unit  #>     <dbl> <chr>                  <chr>      <chr>     <chr>     <chr>      <chr> #>  1 0.347  Adipose_Subcutaneous   UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  2 0.240  Adipose_Visceral_Omen… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  3 0.384  Adrenal_Gland          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  4 0.198  Artery_Aorta           UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  5 0.332  Artery_Coronary        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  6 0.117  Artery_Tibial          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  7 0.631  Bladder                UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  8 0.0347 Brain_Amygdala         UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 98 more rows  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_gene_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $gene #> [1] \"Not enough data. At least three data sets are required for clustering.\" #>  #> $tissue #> [1] \"(((((((((((Cells_Cultured_fibroblasts:0.01,Bladder:0.01):0.01,Prostate:0.02):0.01,(Testis:0.02,Lung:0.02):0.02):0.01,(((((Thyroid:0.01,Minor_Salivary_Gland:0.01):0.01,Uterus:0.01):0.00,(((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.01,Small_Intestine_Terminal_Ileum:0.01):0.00,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.01):0.01):0.00,((Esophagus_Gastroesophageal_Junction:0.00,Adipose_Visceral_Omentum:0.00):0.00,Esophagus_Muscularis:0.01):0.01):0.01,((Ovary:0.00,Nerve_Tibial:0.00):0.01,Esophagus_Mucosa:0.01):0.02):0.01):0.00,(((((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.00,Colon_Transverse:0.01):0.01,Adrenal_Gland:0.02):0.00,(Kidney_Medulla:0.01,Kidney_Cortex:0.01):0.01):0.02):0.01,((((Whole_Blood:0.01,Heart_Left_Ventricle:0.01):0.01,Brain_Cerebellar_Hemisphere:0.02):0.01,(((Colon_Sigmoid:0.01,Brain_Substantia_nigra:0.01):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.01):0.01):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Amygdala:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.01):0.00,Brain_Anterior_cingulate_cortex_BA24:0.01):0.00,Brain_Hippocampus:0.01):0.01,(Artery_Tibial:0.01,Artery_Aorta:0.01):0.01):0.01):0.02):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Brain_Frontal_Cortex_BA9:0.02):0.03,Vagina:0.05):0.02):0.03,((Cervix_Endocervix:0.02,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.04):0.07):0.10,Pancreas:0.20):0.37,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.07,Liver:0.64);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"Find median junction expression data along hierarchical clusters. Returns median junction read counts tissues given gene known transcripts along hierarchical clustering results tissues genes, based junction expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"get_clustered_median_junction_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"# \\dontrun{ get_clustered_median_junction_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 432 × 8 #>    median junctionId           tissueSiteDetailId ontologyId datasetId gencodeId #>     <dbl> <chr>                <chr>              <chr>      <chr>     <chr>     #>  1      0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  2      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  3      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  4      0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  5      0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  6      0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  7      0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  8      0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #>  9      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> 10      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_junction_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $junction #> [1] \"((((((chr1_159713641_159714006:0.03,chr1_159713604_159714002:0.03):0.67,(chr1_159712795_159714006:0.01,chr1_159712581_159713502:0.01):0.69):0.56,chr1_159712795_159713502:1.26):0.90,chr1_159713973_159714498:2.16):0.54,chr1_159714139_159714424:2.70):2.61,chr1_153259734_153260926:5.31);\" #>  #> $tissue #> [1] \"(((((((((((((((((Adipose_Visceral_Omentum:0.00,Adipose_Subcutaneous:0.00):0.00,Artery_Aorta:0.00):0.00,Artery_Coronary:0.00):0.00,Artery_Tibial:0.00):0.00,Brain_Cortex:0.00):0.00,Breast_Mammary_Tissue:0.00):0.00,Colon_Sigmoid:0.00):0.00,Heart_Atrial_Appendage:0.00):0.00,Muscle_Skeletal:0.00):0.00,Nerve_Tibial:0.00):0.00,Vagina:0.00):0.08,Kidney_Medulla:0.08):0.03,(((((((((((((((((((((Brain_Amygdala:0.00,Bladder:0.00):0.00,Brain_Anterior_cingulate_cortex_BA24:0.00):0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Cerebellar_Hemisphere:0.00):0.00,Brain_Cerebellum:0.00):0.00,Brain_Frontal_Cortex_BA9:0.00):0.00,Brain_Hippocampus:0.00):0.00,Brain_Hypothalamus:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Brain_Substantia_nigra:0.00):0.00,Cells_EBV-transformed_lymphocytes:0.00):0.00,Colon_Transverse:0.00):0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Esophagus_Muscularis:0.00):0.00,Heart_Left_Ventricle:0.00):0.00,Kidney_Cortex:0.00):0.00,Pituitary:0.00):0.00,Thyroid:0.00):0.00,Whole_Blood:0.00):0.11):0.03,((((((((((((Cells_Cultured_fibroblasts:0.00,Adrenal_Gland:0.00):0.00,Esophagus_Mucosa:0.00):0.00,Fallopian_Tube:0.00):0.00,Lung:0.00):0.00,Minor_Salivary_Gland:0.00):0.00,Ovary:0.00):0.00,Prostate:0.00):0.00,Small_Intestine_Terminal_Ileum:0.00):0.00,Spleen:0.00):0.00,Stomach:0.00):0.00,Uterus:0.00):0.06,((Cervix_Endocervix:0.00,Cervix_Ectocervix:0.00):0.00,Testis:0.00):0.06):0.09):0.19,Pancreas:0.33):0.27,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.59):0.68,Liver:1.29);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"Find median transcript expression data known transcripts gene along hierarchical clusters. Returns median normalized expression tissues known transcripts given gene along hierarchical clustering results tissues genes, based expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"get_clustered_median_transcript_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"# \\dontrun{ get_clustered_median_transcript_expression(gencodeIds = c(\"ENSG00000203782.5\",                                                     \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` #> # A tibble: 432 × 8 #>    median transcriptId      tissueSiteDetailId    ontologyId datasetId gencodeId #>     <dbl> <chr>             <chr>                 <chr>      <chr>     <chr>     #>  1 0.130  ENST00000255030.9 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  2 0      ENST00000368110.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  3 0      ENST00000368111.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  4 0      ENST00000368112.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  5 0      ENST00000437342.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  6 0.0100 ENST00000473196.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  7 0      ENST00000489317.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #>  9 0      ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> 10 0      ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr>  # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_transcript_expression(c(\"ENSG00000203782.5\",                                                  \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(<df>, 'clusters')` attr(result, \"clusters\") #> $transcript #> [1] \"(((ENST00000473196.1:0.46,ENST00000255030.9:0.46):1.64,(((ENST00000437342.1:0.16,ENST00000368112.5:0.16):0.09,(ENST00000368111.5:0.03,ENST00000368110.1:0.03):0.21):0.15,ENST00000489317.1:0.40):1.70):2.76,ENST00000368742.3:4.86);\" #>  #> $tissue #> [1] \"(((((((((((Spleen:0.00,Breast_Mammary_Tissue:0.00):0.01,Lung:0.01):0.00,((Ovary:0.01,Esophagus_Mucosa:0.01):0.00,Nerve_Tibial:0.01):0.01):0.00,((((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.00,Adipose_Visceral_Omentum:0.01):0.00,((Esophagus_Muscularis:0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Thyroid:0.00):0.00):0.00,(Small_Intestine_Terminal_Ileum:0.01,Artery_Aorta:0.01):0.01):0.00):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Hippocampus:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Artery_Tibial:0.01):0.00,Brain_Amygdala:0.01):0.01,(((Brain_Putamen_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,((Colon_Sigmoid:0.00,Brain_Substantia_nigra:0.00):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00):0.01):0.01):0.01,((((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.01,Kidney_Cortex:0.01):0.00,((Uterus:0.01,Prostate:0.01):0.00,Minor_Salivary_Gland:0.01):0.01):0.00,((((Heart_Left_Ventricle:0.01,Colon_Transverse:0.01):0.00,(Whole_Blood:0.00,Brain_Cerebellar_Hemisphere:0.00):0.01):0.00,((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.01):0.00,Kidney_Medulla:0.02):0.01):0.01):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Vagina:0.02):0.01,(Brain_Frontal_Cortex_BA9:0.01,Brain_Anterior_cingulate_cortex_BA24:0.01):0.02):0.03):0.01,((((Cervix_Endocervix:0.02,Bladder:0.02):0.00,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.03):0.02,Testis:0.05):0.01):0.15,Pancreas:0.21):0.36,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.61,Liver:1.19);\" #>   # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"service returns collapsed exons gene model given gene. Gene-level exon-level expression quantification based GENCODE annotation, collapsed single transcript model gene using algorithm developed GTEx analysis team. default, service queries models used latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"get_collapsed_gene_model_exon(   gencodeId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{  get_collapsed_gene_model_exon(gencodeId = \"ENSG00000132693.12\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   featureType       end genomeBuild chromosome exonNumber geneSymbolUpper exonId #>   <chr>           <int> <chr>       <chr>      <chr>      <chr>           <chr>  #> 1 exon        159714589 GRCh38/hg38 chr1       1          CRP             ENSG0… #> 2 exon        159714138 GRCh38/hg38 chr1       2          CRP             ENSG0… #> # ℹ 7 more variables: datasetId <chr>, start <int>, dataSource <chr>, #> #   gencodeId <chr>, geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Dataset Info — get_dataset_info","title":"Get Dataset Info — get_dataset_info","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Dataset Info — get_dataset_info","text":"","code":"get_dataset_info(datasetId = \"gtex_v8\", organizationName = \"GTEx Consortium\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Dataset Info — get_dataset_info","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Dataset Info — get_dataset_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Dataset Info — get_dataset_info","text":"Note: current returns empty values.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Dataset Info — get_dataset_info","text":"","code":"# \\dontrun{ get_dataset_info() #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Downloads Page Data — get_downloads_page_data","title":"Get Downloads Page Data — get_downloads_page_data","text":"Retrieves files belonging given project_id display Downloads Page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"get_downloads_page_data(project_id = \"adult-gtex\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Downloads Page Data — get_downloads_page_data","text":"project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Downloads Page Data — get_downloads_page_data","text":"Tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Downloads Page Data — get_downloads_page_data","text":"Note: GTEx Portal API documentation states \"GTEx currently one project available: gtex\". However, project_id values \"adult-gtex\" \"egtex\" return results, whereas \"gtex\" (see examples).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"# \\dontrun{  # \"adult-gtex\" (default `project_id` value) and \"egtex\" both return results  get_downloads_page_data() #> # A tibble: 9 × 6 #>   name                         displayName description order parent children     #>   <chr>                        <chr>       <chr>       <int> <chr>  <list>       #> 1 gs://adult-gtex/bulk-gex/    Bulk tissu… \"\"              1 gs://… <named list> #> 2 gs://adult-gtex/bulk-qtl/    QTL         \"\"              2 gs://… <named list> #> 3 gs://adult-gtex/single-cell/ Single cell \"\"              3 gs://… <named list> #> 4 gs://adult-gtex/long-read-d… Long read … \"Long Read…     4 gs://… <named list> #> 5 gs://adult-gtex/haplotype-e… Haplotype … \"Haplotype…     5 gs://… <named list> #> 6 gs://adult-gtex/variants/    Variants    \"\"              6 gs://… <named list> #> 7 gs://adult-gtex/references/  Reference   \"\"              7 gs://… <named list> #> 8 gs://adult-gtex/annotations/ Metadata    \"\"              8 gs://… <named list> #> 9 gs://adult-gtex/additional_… Additional… \"\"              9 gs://… <named list>  egtex <- get_downloads_page_data(\"egtex\")  egtex #> # A tibble: 3 × 6 #>   name                    displayName description      order parent children     #>   <chr>                   <chr>       <chr>            <int> <chr>  <list>       #> 1 gs://egtex/methylation/ Methylation \"\"                   1 gs://… <named list> #> 2 gs://egtex/proteomics/  Proteomics  \"Protein and RN…     2 gs://… <named list> #> 3 gs://egtex/telomeres/   Telomeres   \"Relative telom…     3 gs://… <named list>   # ...\"gtex\" does not  get_downloads_page_data(\"gtex\") #> # A tibble: 0 × 0   # get details for whole blood methylation data, including download URL  purrr::pluck(    egtex$children,    1,    \"folders\",    \"Methylation - EPIC Array\",    \"children\",    \"folders\",    \"mQTLs\",    \"children\",    \"files\",    \"WholeBlood.mQTLs.regular.txt.gz\"  ) #> $displayName #> [1] \"WholeBlood.mQTLs.regular.txt.gz\" #>  #> $description #> [1] \"\" #>  #> $fileSize #> [1] 43461408219 #>  #> $url #> [1] \"https://storage.googleapis.com/egtex/methylation/epic-arrays/mQTLs/WholeBlood.mQTLs.regular.txt.gz\" #>  #> $order #> [1] 27 #>  #> $parent #> [1] \"gs://egtex/methylation/epic-arrays/mQTLs/\" #>  # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Eqtl Genes — get_eqtl_genes","title":"Get Eqtl Genes — get_eqtl_genes","text":"Retrieve eGenes (eQTL Genes). service returns eGenes (eQTL Genes) specified dataset. eGenes genes least one significant cis-eQTL acting upon . Results may filtered tissue. default, service queries latest GTEx release. eGene, results include allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), q-value (qValue). log2AllelicFoldChange allelic fold change (log2 scale) significant eQTL. pValue nominal p-value significant eQTL. pValueThreshold p-value threshold used determine whether cis-eQTL gene significant. details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods. empiricalPValue beta distribution-adjusted empirical p-value FastQTL. qValues calculated based empirical p-values. false discovery rate (FDR) threshold <= 0.05 applied identify genes significant eQTL. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"get_eqtl_genes(   tissueSiteDetailIds,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Eqtl Genes — get_eqtl_genes","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Eqtl Genes — get_eqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"# \\dontrun{ get_eqtl_genes(c(\"Whole_Blood\", \"Artery_Aorta\")) #> Warning: ! Total number of items (24853) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 100 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 24853 #> # A tibble: 250 × 10 #>    tissueSiteDetailId ontologyId  datasetId empiricalPValue gencodeId geneSymbol #>    <chr>              <chr>       <chr>               <dbl> <chr>     <chr>      #>  1 Whole_Blood        UBERON:001… gtex_v8          1.05e- 9 ENSG0000… WASH7P     #>  2 Whole_Blood        UBERON:001… gtex_v8          1.06e-25 ENSG0000… RP11-34P1… #>  3 Whole_Blood        UBERON:001… gtex_v8          6.31e- 2 ENSG0000… CICP27     #>  4 Whole_Blood        UBERON:001… gtex_v8          8.71e- 9 ENSG0000… RP11-34P1… #>  5 Whole_Blood        UBERON:001… gtex_v8          6.01e-20 ENSG0000… RP11-34P1… #>  6 Whole_Blood        UBERON:001… gtex_v8          6.96e- 9 ENSG0000… RP11-34P1… #>  7 Whole_Blood        UBERON:001… gtex_v8          3.10e- 4 ENSG0000… RP11-34P1… #>  8 Whole_Blood        UBERON:001… gtex_v8          1.92e- 3 ENSG0000… ABC7-4304… #>  9 Whole_Blood        UBERON:001… gtex_v8          1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood        UBERON:001… gtex_v8          7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange <dbl>, pValue <dbl>, #> #   pValueThreshold <dbl>, qValue <dbl> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Exons — get_exons","title":"Get Exons — get_exons","text":"service returns exons known transcripts given gene. versioned GENCODE ID required ensure exons single gene. dataset ID GENCODE version genome build must provided. Although annotated exons dataset dependent, specifying dataset equivalent specifying GENCODE version genome build used dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Exons — get_exons","text":"","code":"get_exons(   gencodeId,   gencodeVersion = NULL,   genomeBuild = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Exons — get_exons","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Exons — get_exons","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Exons — get_exons","text":"","code":"# \\dontrun{ get_exons(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #>   featureType       end genomeBuild     start exonId source chromosome gencodeId #>   <chr>           <int> <chr>           <int> <chr>  <chr>  <chr>      <chr>     #> 1 exon        153259733 GRCh38/hg38 153259700 ENSE0… HAVANA chr1       ENSG0000… #> 2 exon        153262122 GRCh38/hg38 153260927 ENSE0… HAVANA chr1       ENSG0000… #> # ℹ 5 more variables: transcriptId <chr>, geneSymbol <chr>, #> #   gencodeVersion <chr>, strand <chr>, exonNumber <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Expression Pca — get_expression_pca","title":"Get Expression Pca — get_expression_pca","text":"Find gene expression PCA data. Returns gene expression PCA (principal component analysis) tissues. Results may filtered tissue, sample, dataset. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Expression Pca — get_expression_pca","text":"","code":"get_expression_pca(   tissueSiteDetailIds,   datasetId = \"gtex_v8\",   sampleId = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Expression Pca — get_expression_pca","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Expression Pca — get_expression_pca","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Expression Pca — get_expression_pca","text":"","code":"# \\dontrun{ get_expression_pca(tissueSiteDetailIds = c(\"Adipose_Subcutaneous\",                                            \"Whole_Blood\")) #> Warning: ! Total number of items (1418) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1418 #> # A tibble: 250 × 7 #>        pc1      pc2      pc3 sampleId    tissueSiteDetailId ontologyId datasetId #>      <dbl>    <dbl>    <dbl> <chr>       <chr>              <chr>      <chr>     #>  1  0.0385 -0.0178   0.0769  GTEX-1117F… Adipose_Subcutane… UBERON:00… gtex_v8   #>  2 -0.0585  0.00809  0.00492 GTEX-111CU… Adipose_Subcutane… UBERON:00… gtex_v8   #>  3  0.140  -0.0308  -0.0368  GTEX-111FC… Adipose_Subcutane… UBERON:00… gtex_v8   #>  4  0.0597  0.140    0.0294  GTEX-111VG… Adipose_Subcutane… UBERON:00… gtex_v8   #>  5 -0.0968  0.00233 -0.0174  GTEX-111YS… Adipose_Subcutane… UBERON:00… gtex_v8   #>  6 -0.120   0.0195  -0.0594  GTEX-1122O… Adipose_Subcutane… UBERON:00… gtex_v8   #>  7 -0.102   0.0652   0.00344 GTEX-1128S… Adipose_Subcutane… UBERON:00… gtex_v8   #>  8  0.105   0.0174  -0.0568  GTEX-113IC… Adipose_Subcutane… UBERON:00… gtex_v8   #>  9 -0.109  -0.0543   0.00594 GTEX-117YX… Adipose_Subcutane… UBERON:00… gtex_v8   #> 10  0.132  -0.0335  -0.0350  GTEX-11DXW… Adipose_Subcutane… UBERON:00… gtex_v8   #> # ℹ 240 more rows  get_expression_pca(tissueSiteDetailIds = \"Adipose_Subcutaneous\",                    sampleId = \"GTEX-1117F-0226-SM-5GZZ7\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #>      pc1     pc2    pc3 sampleId         tissueSiteDetailId ontologyId datasetId #>    <dbl>   <dbl>  <dbl> <chr>            <chr>              <chr>      <chr>     #> 1 0.0385 -0.0178 0.0769 GTEX-1117F-0226… Adipose_Subcutane… UBERON:00… gtex_v8   # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Get File List — get_file_list","title":"Get File List — get_file_list","text":"Get files GTEx dataset Download page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get File List — get_file_list","text":"","code":"get_file_list()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get File List — get_file_list","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get File List — get_file_list","text":"returned tibble includes nested list column, \"filesets\". details files, sub-categorised fileset (see examples section).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get File List — get_file_list","text":"","code":"# \\dontrun{ # Column \"filesets\" is a list column get_file_list() #> # A tibble: 11 × 10 #>    name            subpath dbgapId dataset release order type  id    description #>    <chr>           <chr>   <chr>   <chr>   <chr>   <int> <chr> <chr> <chr>       #>  1 GTEx Analysis … gtex_a… \"phs00… GTEx    v3         10 data… gtex… \"\"          #>  2 GTEx Analysis … gtex_a… \"\"      GTEx    v6p         7 data… gtex… \"The GTEx … #>  3 Biobank Invent… gtex_b… \"\"      GTEx    biobank     5 data… biob… \"\"          #>  4 GTEx Analysis … gtex_a… \"phs00… GTEx    v7          6 data… gtex… \"\"          #>  5 GTEx Analysis … gtex_a… \"phs00… GTEx    v6          8 data… gtex… \"\"          #>  6 Additional Dat… gtex_a… \"\"      GTEx    additi…     3 data… addi… \"\"          #>  7 GTEx Analysis … gtex_a… \"phs00… GTEx    v4          9 data… gtex… \"\"          #>  8 External Datas… gtex_e… \"\"      GTEx    extern…     4 data… exte… \"\"          #>  9 GTEx Analysis … gtex_a… \"phs00… GTEx    v8          1 data… gtex… \"The GTEx … #> 10 eGTEx           gtex_e… \"\"      GTEx    egtex       2 data… egtex \"The Enhan… #> 11 GTEx Analysis … gtex_a… \"phs00… GTEx    v9          0 data… gtex… \"Open-acce… #> # ℹ 1 more variable: filesets <list>  # Get \"GTEx Analysis V9\" file list gtex_v9_files <- get_file_list() |>                    dplyr::filter(name == \"GTEx Analysis V9\") |>                    dplyr::pull(filesets)  # \"GTEx Analysis V9\" filesets names(gtex_v9_files[[1]]) #> [1] \"snRNA-Seq Data\" \"Long Read Data\"  # \"GTEx Analysis V9\", \"snRNA-Seq Data\" fileset files names(gtex_v9_files[[1]][[\"snRNA-Seq Data\"]]$files) #> [1] \"GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad\"        #> [2] \"GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad\" # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Fine Mapping — get_fine_mapping","title":"Get Fine Mapping — get_fine_mapping","text":"Retrieve Fine Mapping Data Finds returns Fine Mapping data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"get_fine_mapping(   gencodeIds,   datasetId = \"gtex_v8\",   variantId = NULL,   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Fine Mapping — get_fine_mapping","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". variantId String. gtex variant ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Fine Mapping — get_fine_mapping","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"# \\dontrun{ # search by gene get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 27 #> # A tibble: 27 × 9 #>    datasetId gencodeId          method     pip setId setSize tissueSiteDetailId #>    <chr>     <chr>              <chr>    <dbl> <int>   <int> <chr>              #>  1 gtex_v8   ENSG00000132693.12 DAP-G  0.0235      1       5 Thyroid            #>  2 gtex_v8   ENSG00000132693.12 DAP-G  0.0221      1       5 Thyroid            #>  3 gtex_v8   ENSG00000132693.12 DAP-G  0.0171      1       5 Thyroid            #>  4 gtex_v8   ENSG00000132693.12 DAP-G  0.0252      1       5 Thyroid            #>  5 gtex_v8   ENSG00000132693.12 DAP-G  0.892       1       5 Thyroid            #>  6 gtex_v8   ENSG00000203782.5  DAP-G  0.0126      1      22 Whole_Blood        #>  7 gtex_v8   ENSG00000203782.5  DAP-G  0.00690     1      22 Whole_Blood        #>  8 gtex_v8   ENSG00000203782.5  DAP-G  0.0313      1      22 Whole_Blood        #>  9 gtex_v8   ENSG00000203782.5  DAP-G  0.00852     1      22 Whole_Blood        #> 10 gtex_v8   ENSG00000203782.5  DAP-G  0.0105      1      22 Whole_Blood        #> # ℹ 17 more rows #> # ℹ 2 more variables: ontologyId <chr>, variantId <chr>  # optionally filter for a single variant and/or one or more tissues get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\"),                  variantId = \"chr1_153228363_A_G_b38\",                  tissueSiteDetailIds = c(\"Whole_Blood\",                                         \"Thyroid\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 9 #>   datasetId gencodeId  method    pip setId setSize tissueSiteDetailId ontologyId #>   <chr>     <chr>      <chr>   <dbl> <int>   <int> <chr>              <chr>      #> 1 gtex_v8   ENSG00000… DAP-G  0.0126     1      22 Whole_Blood        UBERON:00… #> # ℹ 1 more variable: variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"service allows user query full Collapsed Gene Model Exon specific gene gencode ID GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"get_full_get_collapsed_gene_model_exon(gencodeId, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{   get_full_get_collapsed_gene_model_exon(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   featureType       end genomeBuild chromosome exonNumber geneSymbolUpper exonId #>   <chr>           <int> <chr>       <chr>      <chr>      <chr>           <chr>  #> 1 exon        153259733 GRCh38/hg38 chr1       1          LOR             ENSG0… #> 2 exon        153262122 GRCh38/hg38 chr1       2          LOR             ENSG0… #> # ℹ 7 more variables: datasetId <chr>, start <int>, dataSource <chr>, #> #   gencodeId <chr>, geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Functional Annotation — get_functional_annotation","title":"Get Functional Annotation — get_functional_annotation","text":"endpoint retrieves functional annotation certain chromosome location. Default recent dataset release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"get_functional_annotation(   datasetId = \"gtex_v8\",   chromosome,   start,   end,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Functional Annotation — get_functional_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". start Integer. end Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Functional Annotation — get_functional_annotation","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"# \\dontrun{   get_functional_annotation(chromosome = \"chr1\", start = 192168000, end = 192169000) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3 #> # A tibble: 3 × 23 #>   variantId         enhancer promoter openChromatinRegion promoterFlankingRegion #>   <chr>             <lgl>    <lgl>    <lgl>               <lgl>                  #> 1 chr1_192168015_T… TRUE     FALSE    FALSE               FALSE                  #> 2 chr1_192168266_T… TRUE     FALSE    FALSE               FALSE                  #> 3 chr1_192168728_T… FALSE    FALSE    FALSE               FALSE                  #> # ℹ 18 more variables: ctcfBindingSite <lgl>, tfBindingSite <lgl>, #> #   `3PrimeUtrVariant` <lgl>, `5PrimeUtrVariant` <lgl>, #> #   frameshiftVariant <lgl>, intronVariant <lgl>, missenseVariant <lgl>, #> #   nonCodingTranscriptExonVariant <lgl>, spliceAcceptorVariant <lgl>, #> #   spliceDonorVariant <lgl>, spliceRegionVariant <lgl>, stopGained <lgl>, #> #   synonymousVariant <lgl>, chromosome <chr>, pos <int>, ref <chr>, alt <chr>, #> #   datasetId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Expression — get_gene_expression","title":"Get Gene Expression — get_gene_expression","text":"Find normalized gene expression data. Returns normalized gene expression tissues sample level. Results may filtered dataset, gene tissue, least one gene must provided. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Expression — get_gene_expression","text":"","code":"get_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   attributeSubset = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Expression — get_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Expression — get_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Expression — get_gene_expression","text":"","code":"# \\dontrun{   # multiple genes, selected tissues   get_gene_expression(gencodeIds = c(\"ENSG00000132693.12\",                                      \"ENSG00000203782.5\"),                       tissueSiteDetailIds = c(\"Thyroid\", \"Whole_Blood\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… LOR        TPM   #> 2 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… LOR        TPM   #> 3 <dbl [653]> Thyroid            UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 4 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <lgl>    # single gene, selected (single) tissue   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [755]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <lgl>    # subset by sex   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\",                       attributeSubset = \"sex\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 2 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [501]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 2 <dbl [254]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <chr>    # subset by age bracket   get_gene_expression(gencodeIds = \"ENSG00000132693.12\",                       tissueSiteDetailIds = \"Whole_Blood\",                       attributeSubset = \"ageBracket\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 6 × 8 #>   data        tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit  #>   <list>      <chr>              <chr>      <chr>     <chr>     <chr>      <chr> #> 1 <dbl [68]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 2 <dbl [68]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 3 <dbl [113]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 4 <dbl [234]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 5 <dbl [249]> Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 6 <dbl [23]>  Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 1 more variable: subsetGroup <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Search — get_gene_search","title":"Get Gene Search — get_gene_search","text":"Find genes partial complete match gene_id gene_id gene symbol, gencode ID, Ensemble ID Gencode Version Genome Build must specified GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Search — get_gene_search","text":"","code":"get_gene_search(   geneId,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Search — get_gene_search","text":"geneId String. gene symbol, gencode ID, Ensemble ID. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Search — get_gene_search","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Search — get_gene_search","text":"","code":"# \\dontrun{ get_gene_search(\"CRP\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #>   chromosome dataSource description      end gencodeId gencodeVersion geneStatus #>   <chr>      <chr>      <chr>          <int> <chr>     <chr>          <chr>      #> 1 chr1       HAVANA     C-reactive p… 1.60e8 ENSG0000… v26            \"\"         #> 2 chr1       HAVANA     C-reactive p… 1.60e8 ENSG0000… v26            \"\"         #> # ℹ 8 more variables: geneSymbol <chr>, geneSymbolUpper <chr>, geneType <chr>, #> #   genomeBuild <chr>, start <int>, strand <chr>, tss <int>, entrezGeneId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genes — get_genes","title":"Get Genes — get_genes","text":"service returns information reference genes. genome build GENCODE version must provided. Genes searchable gene symbol, GENCODE ID versioned GENCODE ID. Versioned GENCODE ID recommended ensure unique ID matching. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genes — get_genes","text":"","code":"get_genes(   geneIds,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genes — get_genes","text":"geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genes — get_genes","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genes — get_genes","text":"","code":"# \\dontrun{ get_genes(c(\"CRP\", \"IL6R\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #>   chromosome dataSource description    end entrezGeneId gencodeId gencodeVersion #>   <chr>      <chr>      <chr>        <int> <chr>        <chr>     <chr>          #> 1 chr1       HAVANA     interleuki… 1.54e8 3570         ENSG0000… v26            #> 2 chr1       HAVANA     C-reactive… 1.60e8 1401         ENSG0000… v26            #> # ℹ 8 more variables: geneStatus <chr>, geneSymbol <chr>, #> #   geneSymbolUpper <chr>, geneType <chr>, genomeBuild <chr>, start <int>, #> #   strand <chr>, tss <int> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genomic Features — get_genomic_features","title":"Get Genomic Features — get_genomic_features","text":"GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genomic Features — get_genomic_features","text":"","code":"get_genomic_features(.featureId, datasetId = \"gtex_v8\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genomic Features — get_genomic_features","text":".featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genomic Features — get_genomic_features","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Genomic Features — get_genomic_features","text":"endpoint takes path parameter \"featureId\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genomic Features — get_genomic_features","text":"","code":"# \\dontrun{ # gene symbol get_genomic_features(\"brca1\") #> # A tibble: 1 × 17 #>   gencodeVersion      end description     geneSymbolUpper genomeBuild geneStatus #>   <chr>             <int> <chr>           <chr>           <chr>       <chr>      #> 1 v26            43170245 BRCA1, DNA rep… BRCA1           GRCh38/hg38 \"\"         #> # ℹ 11 more variables: strand <chr>, entrezGeneId <int>, geneType <chr>, #> #   start <int>, dataSource <chr>, gencodeId <chr>, geneSymbol <chr>, #> #   tss <int>, chromosome <chr>, featureType <chr>, assembly <chr>  # GENCODE ID get_genomic_features(\"ENSG00000132693.12\") #> # A tibble: 1 × 17 #>   gencodeVersion       end description    geneSymbolUpper genomeBuild geneStatus #>   <chr>              <int> <chr>          <chr>           <chr>       <chr>      #> 1 v26            159714589 C-reactive pr… CRP             GRCh38/hg38 \"\"         #> # ℹ 11 more variables: strand <chr>, entrezGeneId <int>, geneType <chr>, #> #   start <int>, dataSource <chr>, gencodeId <chr>, geneSymbol <chr>, #> #   tss <int>, chromosome <chr>, featureType <chr>, assembly <chr>  # RSID get_genomic_features(\"rs1815739\") #> # A tibble: 1 × 8 #>   featureType chromosome    start snpId     variantId       ref   alt   assembly #>   <chr>       <chr>         <int> <chr>     <chr>           <chr> <chr> <chr>    #> 1 snp         chr11      66560624 rs1815739 chr11_66560624… C     T     HG38      # GTEx variant ID get_genomic_features(\"chr11_66561023_G_GTTA_b38\") #> # A tibble: 1 × 8 #>   featureType chromosome    start snpId     variantId       ref   alt   assembly #>   <chr>       <chr>         <int> <chr>     <chr>           <chr> <chr> <chr>    #> 1 snp         chr11      66561023 rs3837428 chr11_66561023… G     GTTA  HG38     # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"Find GWAS Catalog certain chromosome start end locations. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"get_gwas_catalog_by_location(   start,   end,   chromosome,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"# \\dontrun{ get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = \"chr1\") #> Warning: ! Total number of items (316) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 316 #> # A tibble: 250 × 10 #>    chromosome   start     end phenotype  pValue   beta pubmedId snpId riskAllele #>    <chr>        <int>   <int> <chr>       <dbl>  <dbl>    <int> <chr> <chr>      #>  1 chr1       9653328 9653329 Testicula…  6e-13 1.14   28604728 rs42… T          #>  2 chr1       8428505 8428506 Autism sp…  7e- 9 1.06   28540026 rs30… ?          #>  3 chr1       9651584 9651585 Monocyte …  2e- 9 0.0222 27863252 rs75… G          #>  4 chr1       3080038 3080039 Mean corp…  1e-13 0.0311 27863252 rs15… C          #>  5 chr1       3811497 3811498 Mean corp…  1e-13 0.0301 27863252 rs12… T          #>  6 chr1       4544044 4544045 Adolescen…  3e- 9 1.2    26394188 rs24… ?          #>  7 chr1       1312114 1312115 Inflammat…  8e-13 1.10   23128233 rs12… A          #>  8 chr1       7961913 7961914 Inflammat…  1e-15 1.11   23128233 rs35… G          #>  9 chr1       8444361 8444362 Eosinophi…  2e-19 0.0328 27863252 rs15… A          #> 10 chr1       9281727 9281728 Eosinophi…  1e-10 0.0260 27863252 rs67… T          #> # ℹ 240 more rows #> # ℹ 1 more variable: genomeBuild <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Image — get_image","title":"Get Image — get_image","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Image — get_image","text":"","code":"get_image(tissueSampleIds = NULL, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Image — get_image","text":"tissueSampleIds Array strings. list Tissue Sample ID(s). page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Image — get_image","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Image — get_image","text":"","code":"# \\dontrun{ get_image() #> Warning: ! Total number of items (25713) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 103 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25713 #> # A tibble: 250 × 11 #>    ageBracket hardyScale hide  histologyImageId pathologyNotes   sex   subjectId #>    <chr>      <chr>      <lgl> <chr>            <chr>            <chr> <chr>     #>  1 60-69      Slow death FALSE GTEX-1117F-0126  6 pieces, minim… fema… GTEX-111… #>  2 60-69      Slow death FALSE GTEX-1117F-0226  2 pieces, ~15% … fema… GTEX-111… #>  3 60-69      Slow death FALSE GTEX-1117F-0326  2 pieces, clean… fema… GTEX-111… #>  4 60-69      Slow death FALSE GTEX-1117F-0426  2 pieces, !5% f… fema… GTEX-111… #>  5 60-69      Slow death FALSE GTEX-1117F-0526  2 pieces, clean… fema… GTEX-111… #>  6 60-69      Slow death FALSE GTEX-1117F-0626  2 pieces, up to… fema… GTEX-111… #>  7 60-69      Slow death FALSE GTEX-1117F-0726  2 pieces, no ab… fema… GTEX-111… #>  8 60-69      Slow death FALSE GTEX-1117F-0826  2 pieces, exten… fema… GTEX-111… #>  9 60-69      Slow death FALSE GTEX-1117F-0926  6 pieces, adher… fema… GTEX-111… #> 10 60-69      Slow death FALSE GTEX-1117F-1026  2 pieces, moder… fema… GTEX-111… #> # ℹ 240 more rows #> # ℹ 4 more variables: tissueSiteDetail <chr>, sampleId <chr>, #> #   tissueSampleId <chr>, pathologyNotesCategories <tibble[,31]>  # filter by `tissueSampleId` result <- get_image(tissueSampleIds = \"GTEX-1117F-0526\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 print(result) #> # A tibble: 1 × 11 #>   ageBracket hardyScale hide  histologyImageId pathologyNotes                    #>   <chr>      <chr>      <lgl> <chr>            <chr>                             #> 1 60-69      Slow death FALSE GTEX-1117F-0526  2 pieces, clean, Monckebeg media… #> # ℹ 6 more variables: pathologyNotesCategories <tibble[,2]>, sampleId <chr>, #> #   sex <chr>, subjectId <chr>, tissueSampleId <chr>, tissueSiteDetail <chr>  # note that `pathologyNotesCategories` (if present) is a list column print(result$pathologyNotesCategories) #> # A tibble: 1 × 2 #>   monckeberg sclerotic #>   <lgl>      <lgl>     #> 1 TRUE       TRUE      # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Independent Eqtl — get_independent_eqtl","title":"Get Independent Eqtl — get_independent_eqtl","text":"Retrieve Independent eQTL Data Finds returns Independent eQTL Data data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"get_independent_eqtl(   gencodeIds,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Independent Eqtl — get_independent_eqtl","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Independent Eqtl — get_independent_eqtl","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"# \\dontrun{ # search by gene get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\",                                \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 8 #> # A tibble: 8 × 14 #>   gencodeId       geneSymbol variantId snpId tissueSiteDetailId ontologyId  rank #>   <chr>           <chr>      <chr>     <chr> <chr>              <chr>      <int> #> 1 ENSG0000013269… CRP        chr1_160… rs66… Esophagus_Gastroe… UBERON:00…     1 #> 2 ENSG0000013269… CRP        chr1_159… rs57… Thyroid            UBERON:00…     1 #> 3 ENSG0000020378… LOR        chr1_153… rs14… Artery_Coronary    UBERON:00…     1 #> 4 ENSG0000020378… LOR        chr1_153… rs87… Whole_Blood        UBERON:00…     1 #> 5 ENSG0000020378… LOR        chr1_153… rs12… Skin_Sun_Exposed_… UBERON:00…     1 #> 6 ENSG0000020378… LOR        chr1_152… rs77… Heart_Atrial_Appe… UBERON:00…     1 #> 7 ENSG0000020378… LOR        chr1_153… rs12… Esophagus_Mucosa   UBERON:00…     1 #> 8 ENSG0000013269… CRP        chr1_159… rs86… Muscle_Skeletal    UBERON:00…     1 #> # ℹ 7 more variables: tssDistance <int>, maf <dbl>, pValue <dbl>, nes <dbl>, #> #   chromosome <chr>, pos <int>, datasetId <chr>  # optionally filter for a single variant and/or one or more tissues get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\",                                     \"ENSG00000203782.5\"),                      tissueSiteDetailIds = c(\"Whole_Blood\",                                              \"Thyroid\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #>   gencodeId       geneSymbol variantId snpId tissueSiteDetailId ontologyId  rank #>   <chr>           <chr>      <chr>     <chr> <chr>              <chr>      <int> #> 1 ENSG0000013269… CRP        chr1_159… rs57… Thyroid            UBERON:00…     1 #> 2 ENSG0000020378… LOR        chr1_153… rs87… Whole_Blood        UBERON:00…     1 #> # ℹ 7 more variables: tssDistance <int>, maf <dbl>, pValue <dbl>, nes <dbl>, #> #   chromosome <chr>, pos <int>, datasetId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"Find linkage disequilibrium (LD) data given variant GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(   variantId,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"variantId String. gtex variant ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(\"chr1_159245536_C_T_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 241 #> # A tibble: 241 × 3 #>    variantId_1             variantId_2               ld #>    <chr>                   <chr>                  <dbl> #>  1 chr1_159163610_GA_G_b38 chr1_159245536_C_T_b38 0.114 #>  2 chr1_159163924_G_A_b38  chr1_159245536_C_T_b38 0.114 #>  3 chr1_159164864_T_C_b38  chr1_159245536_C_T_b38 0.114 #>  4 chr1_159165054_A_G_b38  chr1_159245536_C_T_b38 0.113 #>  5 chr1_159165563_T_C_b38  chr1_159245536_C_T_b38 0.113 #>  6 chr1_159174791_T_C_b38  chr1_159245536_C_T_b38 0.252 #>  7 chr1_159176518_G_T_b38  chr1_159245536_C_T_b38 0.146 #>  8 chr1_159176900_C_A_b38  chr1_159245536_C_T_b38 0.271 #>  9 chr1_159177147_A_T_b38  chr1_159245536_C_T_b38 0.274 #> 10 chr1_159179691_T_C_b38  chr1_159245536_C_T_b38 0.253 #> # ℹ 231 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"Find linkage disequilibrium (LD) data given gene. endpoint returns linkage disequilibrium data cis-eQTLs found associated provided gene specified dataset. Results queried gencode ID. default, service queries latest GTEx release. Specify dataset ID fetch results different dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(   gencodeId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(gencodeId = \"ENSG00000132693.12\") #> Warning: ! Total number of items (3558) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 15 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3558 #> # A tibble: 250 × 3 #>    variantId_1            variantId_2                         ld #>    <chr>                  <chr>                            <dbl> #>  1 chr1_159230230_G_T_b38 chr1_159230339_A_C_b38           1     #>  2 chr1_159230230_G_T_b38 chr1_159245536_C_T_b38           0.971 #>  3 chr1_159230230_G_T_b38 chr1_159302270_T_C_b38           0.717 #>  4 chr1_159230230_G_T_b38 chr1_159343657_A_T_b38           0.302 #>  5 chr1_159230230_G_T_b38 chr1_159344052_G_A_b38           0.300 #>  6 chr1_159230230_G_T_b38 chr1_159347493_G_A_b38           0.300 #>  7 chr1_159230230_G_T_b38 chr1_159350390_C_A_b38           0.300 #>  8 chr1_159230230_G_T_b38 chr1_159351189_G_A_b38           0.300 #>  9 chr1_159230230_G_T_b38 chr1_159359256_C_A_b38           0.302 #> 10 chr1_159230230_G_T_b38 chr1_159360755_ATACATAAGTG_A_b38 0.300 #> # ℹ 240 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Maintenance Message — get_maintenance_message","title":"Get Maintenance Message — get_maintenance_message","text":"Getting maintenance messages database enabled. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"get_maintenance_message(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Maintenance Message — get_maintenance_message","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Maintenance Message — get_maintenance_message","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Maintenance Message — get_maintenance_message","text":"Note typically returns empty tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"# \\dontrun{ get_maintenance_message() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 0 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 0 #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Exon Expression — get_median_exon_expression","title":"Get Median Exon Expression — get_median_exon_expression","text":"Find median exon expression data. Returns median exon read counts, tissues, collapsed gene model. Results may filtered dataset, gene tissue, least one gene must provided default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"get_median_exon_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Exon Expression — get_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Exon Expression — get_median_exon_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"# \\dontrun{ # median exon expression values for CRP, filtered for whole blood get_median_exon_expression(gencodeIds = \"ENSG00000132693.12\",                            tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 8 #>   median exonId     tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #>    <dbl> <chr>      <chr>              <chr>      <chr>     <chr>     <chr>      #> 1      0 ENSG00000… Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        #> 2      5 ENSG00000… Whole_Blood        UBERON:00… gtex_v8   ENSG0000… CRP        #> # ℹ 1 more variable: unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Gene Expression — get_median_gene_expression","title":"Get Median Gene Expression — get_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"get_median_gene_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Gene Expression — get_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Gene Expression — get_median_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"# \\dontrun{ get_median_gene_expression(gencodeIds = \"ENSG00000132693.12\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 7 #>    median tissueSiteDetailId     ontologyId datasetId gencodeId geneSymbol unit  #>     <dbl> <chr>                  <chr>      <chr>     <chr>     <chr>      <chr> #>  1 0.347  Adipose_Subcutaneous   UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  2 0.240  Adipose_Visceral_Omen… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  3 0.384  Adrenal_Gland          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  4 0.198  Artery_Aorta           UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  5 0.332  Artery_Coronary        UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  6 0.117  Artery_Tibial          UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  7 0.631  Bladder                UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  8 0.0347 Brain_Amygdala         UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #>  9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8   ENSG0000… CRP        TPM   #> # ℹ 44 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Junction Expression — get_median_junction_expression","title":"Get Median Junction Expression — get_median_junction_expression","text":"Find junction gene expression data. Returns median junction read counts tissues given gene known transcripts. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"get_median_junction_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Junction Expression — get_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Junction Expression — get_median_junction_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"# \\dontrun{ get_median_junction_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #>    median junctionId           tissueSiteDetailId ontologyId datasetId gencodeId #>     <dbl> <chr>                <chr>              <chr>      <chr>     <chr>     #>  1      0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  2      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  3      0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  4      0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  5      0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  6      0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  7      0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8   ENSG0000… #>  8      0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #>  9      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> 10      0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Transcript Expression — get_median_transcript_expression","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"Find median transcript expression data known transcripts gene. Returns median normalized expression tissues known transcripts given gene. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"get_median_transcript_expression(   gencodeIds,   datasetId = \"gtex_v8\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"# \\dontrun{ get_median_transcript_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #>    median transcriptId      tissueSiteDetailId    ontologyId datasetId gencodeId #>     <dbl> <chr>             <chr>                 <chr>      <chr>     <chr>     #>  1 0.130  ENST00000255030.9 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  2 0      ENST00000368110.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  3 0      ENST00000368111.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  4 0      ENST00000368112.5 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  5 0      ENST00000437342.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  6 0.0100 ENST00000473196.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  7 0      ENST00000489317.1 Adipose_Subcutaneous  UBERON:00… gtex_v8   ENSG0000… #>  8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #>  9 0      ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> 10 0      ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8   ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol <chr>, unit <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"Find multi-tissue eQTL Metasoft results. service returns multi-tissue eQTL Metasoft results given gene variant specified dataset. Versioned GENCODE ID must provided. tissue, results include: m-value (mValue), normalized effect size (nes), p-value (pValue), standard error (se). m-value posterior probability eQTL effect exists tissue tested cross-tissue meta-analysis (Han Eskin, PLoS Genetics 8(3): e1002555, 2012). normalized effect size slope linear regression normalized expression data versus three genotype categories using single-tissue eQTL analysis, representing eQTL effect size. p-value t-test compares observed NES single-tissue eQTL analysis null NES 0. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"get_multi_tissue_eqtls(   gencodeIds,   variantId = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_multi_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\",                                      \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 132 #> # A tibble: 6,468 × 5 #>    gencodeId         datasetId   metaP variantId              tissues          #>    <chr>             <chr>       <dbl> <chr>                  <named list>     #>  1 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  2 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  3 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  4 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  5 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  6 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  7 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  8 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #>  9 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #> 10 ENSG00000203782.5 gtex_v8   0.00177 chr1_152346526_G_T_b38 <named list [4]> #> # ℹ 6,458 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Neighbor Gene — get_neighbor_gene","title":"Get Neighbor Gene — get_neighbor_gene","text":"Find neighboring genes certain chromosome around position certain window size. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"get_neighbor_gene(pos, chromosome, bp_window, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Neighbor Gene — get_neighbor_gene","text":"pos Integer, vector. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". bp_window Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Neighbor Gene — get_neighbor_gene","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"# \\dontrun{ get_neighbor_gene(pos = 1000000, chromosome = \"chr1\", bp_window = 10000) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 15 #>   chromosome dataSource description      end gencodeId gencodeVersion geneStatus #>   <chr>      <chr>      <chr>          <int> <chr>     <chr>          <chr>      #> 1 chr1       HAVANA     novel transc… 9.98e5 ENSG0000… v26            \"\"         #> 2 chr1       HAVANA     hes family b… 1.00e6 ENSG0000… v26            \"\"         #> 3 chr1       HAVANA     ISG15 ubiqui… 1.01e6 ENSG0000… v26            \"\"         #> 4 chr1       HAVANA     ribosomal pr… 1.01e6 ENSG0000… v26            \"\"         #> # ℹ 8 more variables: geneSymbol <chr>, geneSymbolUpper <chr>, geneType <chr>, #> #   genomeBuild <chr>, start <int>, strand <chr>, tss <int>, entrezGeneId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":null,"dir":"Reference","previous_headings":"","what":"Get News Item — get_news_item","title":"Get News Item — get_news_item","text":"Getting news items database current. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get News Item — get_news_item","text":"","code":"get_news_item(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get News Item — get_news_item","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get News Item — get_news_item","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get News Item — get_news_item","text":"","code":"# \\dontrun{ get_news_item() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 23 #> # A tibble: 23 × 6 #>    title                                newsText  rank dateCreated release    id #>    <chr>                                <chr>    <int> <chr>       <chr>   <int> #>  1 New Top 50 Expressed Genes Visualiz… \"The GT…   240 2018-04-04  news_i…   240 #>  2 New Multi-Gene Query Visualization   \"The GT…   250 2018-04-04  news_i…   250 #>  3 New eQTL Dashboard Visualization     \"The GT…   260 2018-04-04  news_i…   260 #>  4 Video Tutorial for the Gene-eQTL Vi… \"Watch …   270 2018-04-05  news_i…   270 #>  5 Access GTEx Biospecimens Here        \"We hav…   280 2018-05-10  news_i…   280 #>  6 Access GTEx Data Programmatically w… \"You ca…   290 2018-09-20  news_i…   290 #>  7 Reuse GTEx Visualizations On Your W… \"You ca…   300 2018-09-20  news_i…   300 #>  8 Use The GTEx Portal On Your Phone    \"We hav…   310 2018-09-20  news_i…   310 #>  9 GTEx Portal Visualizations Updated   \"We hav…   320 2018-12-06  news_i…   320 #> 10 Help Us Help You: New Feature Survey \"PLEASE…   331 2019-02-06  news_i…   331 #> # ℹ 13 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Biobank Data) — get_sample_biobank_data","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"get_sample_biobank_data(   draw = NULL,   materialTypes = NULL,   tissueSiteDetailIds = NULL,   pathCategory = NULL,   tissueSampleIds = NULL,   sex = NULL,   sortBy = \"sampleId\",   sortDirection = \"asc\",   searchTerm = NULL,   sampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"draw Integer. materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"# \\dontrun{  get_sample_biobank_data(tissueSiteDetailIds = \"Whole_Blood\") #> Warning: ! Total number of items (1329) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems (recordsFiltered) = 1329 #> • recordsTotal = 72513 #> # A tibble: 250 × 26 #>    materialType    sampleId       sampleIdUpper sex   hasGTExImage concentration #>    <chr>           <chr>          <chr>         <chr> <lgl>                <dbl> #>  1 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               190.   #>  2 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               154    #>  3 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE                41.2  #>  4 DNA:DNA Genomic GTEX-111CU-00… GTEX-111CU-0… male  FALSE                85.9  #>  5 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                96.0  #>  6 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                95.3  #>  7 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE               142.   #>  8 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE                 4.35 #>  9 RNA:Total RNA   GTEX-111FC-00… GTEX-111FC-0… male  FALSE               128.   #> 10 RNA:Total RNA   GTEX-111FC-00… GTEX-111FC-0… male  FALSE               128.   #> # ℹ 240 more rows #> # ℹ 20 more variables: analysisRelease <chr>, genotype <chr>, hardyScale <chr>, #> #   pathologyNotes <chr>, subjectId <chr>, tissueSiteDetailId <chr>, #> #   hasGenotype <lgl>, originalMaterialType <chr>, aliquotId <chr>, #> #   tissueSampleId <chr>, ageBracket <chr>, brainTissueDonor <lgl>, #> #   volume <dbl>, hasExpressionData <lgl>, hasBRDImage <lgl>, #> #   tissueSiteDetail <chr>, amount <dbl>, mass <dbl>, tissueSite <chr>, … # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"service returns information samples used analyses datasets. Results may filtered dataset ID, sample ID, subject ID, sample metadata, provided parameters. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"get_sample_datasets_endpoints(   datasetId = \"gtex_v8\",   sampleIds = NULL,   tissueSampleIds = NULL,   subjectIds = NULL,   ageBrackets = NULL,   sex = NULL,   pathCategory = NULL,   tissueSiteDetailId = NULL,   aliquotIds = NULL,   autolysisScores = NULL,   hardyScales = NULL,   ischemicTime = NULL,   ischemicTimeGroups = NULL,   rin = NULL,   uberonIds = NULL,   dataTypes = NULL,   sortBy = NULL,   sortDirection = NULL,   page = NULL,   itemsPerPage = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleIds Character vector. GTEx sample ID. tissueSampleIds Array strings. list Tissue Sample ID(s). subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". sex String. Options: \"male\", \"female\". pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. aliquotIds Character vector. autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". rin Integer vector. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"# \\dontrun{  get_sample_datasets_endpoints() #> Warning: ! Total number of items (22734) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 91 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 22734 #> # A tibble: 10,946 × 20 #>    ischemicTime aliquotId tissueSampleId       tissueSiteDetail         dataType #>           <int> <chr>     <chr>                <chr>                    <chr>    #>  1         1188 SM-58Q7G  GTEX-1117F-0003      Whole Blood              WES      #>  2         1188 SM-5DWSB  GTEX-1117F-0003      Whole Blood              OMNI     #>  3         1188 SM-6WBT7  GTEX-1117F-0003      Whole Blood              WGS      #>  4         1193 SM-AHZ7F  GTEX-1117F-0011-R10a Brain - Frontal Cortex … NA       #>  5         1193 SM-CYKQ8  GTEX-1117F-0011-R10b Brain - Frontal Cortex … NA       #>  6         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  7         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  8         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #>  9         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #> 10         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ   #> # ℹ 10,936 more rows #> # ℹ 15 more variables: ischemicTimeGroup <chr>, freezeType <chr>, #> #   sampleId <chr>, sampleIdUpper <chr>, ageBracket <chr>, hardyScale <chr>, #> #   tissueSiteDetailId <chr>, subjectId <chr>, uberonId <chr>, sex <chr>, #> #   datasetId <chr>, rin <chr>, pathologyNotesCategories <named list>, #> #   pathologyNotes <chr>, autolysisScore <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Service Info — get_service_info","title":"Get Service Info — get_service_info","text":"General information GTEx service. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Service Info — get_service_info","text":"","code":"get_service_info()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Service Info — get_service_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Service Info — get_service_info","text":"","code":"# \\dontrun{ get_service_info() #> # A tibble: 1 × 9 #>   id     name  version organization_name organization_url description contactUrl #>   <chr>  <chr> <chr>   <chr>             <chr>            <chr>       <chr>      #> 1 org.g… GTEx… 2.0.0   GTEx Project      https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl <chr>, environment <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Find significant single tissue eQTLs. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, gene, variant dataset. search gene, use versioned GENCODE ID. search variant, use dbSNP rs ID (snpId). default, service queries latest GTEx release retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"get_significant_single_tissue_eqtls(   gencodeIds = NULL,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Note: although GTEx Portal API documentation says use dbSNP rsID searching variant, returns results. Instead use gtex variant IDs e.g. use \"chr1_153209640_C_A_b38\" instead \"rs1410858\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs12128960 159343657 RS12128960 chr1_1593… CRP        8.52e-5 CRP             #>  2 rs12132451 159344052 RS12132451 chr1_1593… CRP        7.92e-5 CRP             #>  3 rs12136402 159347493 RS12136402 chr1_1593… CRP        7.92e-5 CRP             #>  4 rs10908709 159350390 RS10908709 chr1_1593… CRP        7.92e-5 CRP             #>  5 rs10908710 159351189 RS10908710 chr1_1593… CRP        7.92e-5 CRP             #>  6 rs11265178 159359256 RS11265178 chr1_1593… CRP        9.62e-5 CRP             #>  7 rs35532309 159360755 RS35532309 chr1_1593… CRP        6.11e-5 CRP             #>  8 rs6692378  159369451 RS6692378  chr1_1593… CRP        1.17e-6 CRP             #>  9 rs10908714 159370563 RS10908714 chr1_1593… CRP        1.80e-5 CRP             #> 10 rs6656924  159372915 RS6656924  chr1_1593… CRP        1.00e-6 CRP             #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>  # search by variant - must be variantId (not rsid) get_significant_single_tissue_eqtls(variantIds = \"chr1_153209640_C_A_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #>   snpId           pos snpIdUpper variantId   geneSymbol   pValue geneSymbolUpper #>   <chr>         <int> <chr>      <chr>       <chr>         <dbl> <chr>           #> 1 rs1410858 153209640 RS1410858  chr1_15320… LOR        5.47e- 5 LOR             #> 2 rs1410858 153209640 RS1410858  chr1_15320… PRR9       5.35e-19 PRR9            #> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>  # filter by gene/variant and tissue site - either `gencodeIds` or `variantIds` # should be supplied as a minimum get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\",                                                   \"ENSG00000203782.5\"),                                     variantIds = \"chr1_153209640_C_A_b38\",                                     tissueSiteDetailIds = \"Whole_Blood\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 13 #>   snpId    pos snpIdUpper variantId geneSymbol  pValue geneSymbolUpper datasetId #>   <chr>  <int> <chr>      <chr>     <chr>        <dbl> <chr>           <chr>     #> 1 rs14… 1.53e8 RS1410858  chr1_153… LOR        5.47e-5 LOR             gtex_v8   #> # ℹ 5 more variables: tissueSiteDetailId <chr>, ontologyId <chr>, #> #   chromosome <chr>, gencodeId <chr>, nes <dbl> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"Find significant single tissue eQTLs using Chromosomal Locations. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, /dataset. default, service queries latest GTEx release. Since endpoint used support third party program portal, return structure different endpoints paginated. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"get_significant_single_tissue_eqtls_by_location(   tissueSiteDetailId,   start,   end,   chromosome,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"# \\dontrun{ get_significant_single_tissue_eqtls_by_location(   tissueSiteDetailId = \"Artery_Aorta\",   start = 10000,   end = 250000,   chromosome = \"chr11\") #> # A tibble: 434 × 11 #>    chromosome datasetId gencodeId      geneSymbol geneSymbolUpper   nes   pValue #>    <chr>      <chr>     <chr>          <chr>      <chr>           <dbl>    <dbl> #>  1 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.381 1.11e- 6 #>  2 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.364 2.25e- 6 #>  3 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.417 3.10e- 8 #>  4 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.480 8.39e- 9 #>  5 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #>  6 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.553 8.89e-10 #>  7 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.577 2.95e-12 #>  8 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.547 6.13e-10 #>  9 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #> 10 chr11      gtex_v8   ENSG000001779… BET1L      BET1L           0.462 6.36e- 9 #> # ℹ 424 more rows #> # ℹ 4 more variables: pos <int>, snpId <chr>, tissueSiteDetailId <chr>, #> #   variantId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"Retrieve Interaction eQTL Data. service returns cell type interaction eQTLs (ieQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"get_significant_single_tissue_ieqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_ieqtls(c(\"ENSG00000132693.12\",                                        \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 86 #> # A tibble: 86 × 24 #>    snpId     bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #>    <chr>     <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>           #>  1 rs34188… 0.0890 1.54e8 RS34188388  0.102  0.00447  LOR        LOR             #>  2 rs24945… 0.0654 1.60e8 RS2494523   0.867  0.00129  CRP        CRP             #>  3 rs986760 0.148  1.53e8 RS986760    0.0454 0.00694  LOR        LOR             #>  4 rs17697… 0.0428 1.59e8 RS17697329  0.515  0.000627 CRP        CRP             #>  5 rs67415… 0.154  1.53e8 RS67415955  0.565  0.000754 LOR        LOR             #>  6 rs12133… 0.157  1.60e8 RS12133356  0.634  0.00106  CRP        CRP             #>  7 rs12132… 0.113  1.53e8 RS12132927  0.858  0.00365  LOR        LOR             #>  8 rs30269… 0.0683 1.59e8 RS3026943   0.684  0.00222  CRP        CRP             #>  9 rs24946… 0.0567 1.54e8 RS2494670   0.516  0.000595 LOR        LOR             #> 10 rs12121… 0.0695 1.60e8 RS12121609  0.444  0.000266 CRP        CRP             #> # ℹ 76 more rows #> # ℹ 16 more variables: pValueI <dbl>, bGI <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, tissueCellType <chr>, #> #   tssDistance <int>, bGSE <dbl>, variantId <chr>, maf <dbl>, bISE <dbl>, #> #   datasetId <chr>, bG <dbl>, pValueAdjustedBH <dbl>, bI <dbl>, #> #   gencodeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"Retrieve Interaction sQTL Data. service retrieves cell type interaction sQTLs (isQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"get_significant_single_tissue_isqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_isqtls(gencodeIds = c(\"ENSG00000065613.9\",                                                     \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 25 #>   snpId      bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #>   <chr>      <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>           #> 1 rs4845790 0.0194 1.53e8 RS4845790  0.00645  8.97e-7 LOR        LOR             #> 2 rs4845790 0.0196 1.53e8 RS4845790  0.0118   1.41e-7 LOR        LOR             #> 3 rs359327… 0.0289 1.54e8 RS35932716 0.0142   3.70e-5 LOR        LOR             #> 4 rs146285… 0.0293 1.53e8 RS1462851… 0.0225   3.03e-5 LOR        LOR             #> # ℹ 17 more variables: pValueI <dbl>, bGI <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, tissueCellType <chr>, #> #   tssDistance <int>, bGSE <dbl>, variantId <chr>, maf <dbl>, bISE <dbl>, #> #   datasetId <chr>, bG <dbl>, pValueAdjustedBH <dbl>, bI <dbl>, #> #   gencodeId <chr>, phenotypeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"Retrieve Single Tissue sQTL Data. service returns single tissue sQTL data given genes, specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"get_significant_single_tissue_sqtls(   gencodeIds,   variantIds = NULL,   tissueSiteDetailIds = NULL,   datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_sqtls(gencodeIds = c(\"ENSG00000065613.9\",                                                    \"ENSG00000203782.5\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 176 #> # A tibble: 176 × 14 #>    snpId            pos snpIdUpper variantId  geneSymbol  pValue geneSymbolUpper #>    <chr>          <int> <chr>      <chr>      <chr>        <dbl> <chr>           #>  1 rs4636462  152442732 RS4636462  chr1_1524… LOR        7.71e-5 LOR             #>  2 rs4845768  152442997 RS4845768  chr1_1524… LOR        6.57e-5 LOR             #>  3 rs12069640 152444300 RS12069640 chr1_1524… LOR        7.13e-5 LOR             #>  4 rs11803629 152445670 RS11803629 chr1_1524… LOR        1.81e-4 LOR             #>  5 rs12125681 152445737 RS12125681 chr1_1524… LOR        1.81e-4 LOR             #>  6 rs11205004 152446586 RS11205004 chr1_1524… LOR        1.81e-4 LOR             #>  7 rs11579085 152447965 RS11579085 chr1_1524… LOR        1.81e-4 LOR             #>  8 rs1885529  152448570 RS1885529  chr1_1524… LOR        1.81e-4 LOR             #>  9 rs1885528  152448978 RS1885528  chr1_1524… LOR        1.81e-4 LOR             #> 10 rs1885527  152449069 RS1885527  chr1_1524… LOR        1.81e-4 LOR             #> # ℹ 166 more rows #> # ℹ 7 more variables: datasetId <chr>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>, #> #   phenotypeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleux Gex — get_single_nucleus_gex","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"Retrieve Single Nucleus Gene Expression Data given Gene. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"get_single_nucleus_gex(   gencodeIds,   datasetId = \"gtex_snrnaseq_pilot\",   tissueSiteDetailIds = NULL,   excludeDataArray = TRUE,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. excludeDataArray String. Options TRUE FALSE page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"# \\dontrun{ # Search for one or more genes - returns a tibble with one row per tissue. # Column \"cellTypes\" now contains a tibble of expression summary data, with # one row for each cell type get_single_nucleus_gex(gencodeIds = c(\"ENSG00000203782.5\",                                       \"ENSG00000132693.12\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 14 #> # A tibble: 14 × 7 #>    tissueSiteDetailId  ontologyId datasetId gencodeId geneSymbol cellTypes unit  #>    <chr>               <chr>      <chr>     <chr>     <chr>      <list>    <chr> #>  1 Muscle_Skeletal     UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  2 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  3 Esophagus_Mucosa    UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  4 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  5 Lung                UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  6 Prostate            UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  7 Skin_Sun_Exposed_L… UBERON:00… gtex_snr… ENSG0000… LOR        <tibble>  log(… #>  8 Muscle_Skeletal     UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #>  9 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 10 Esophagus_Mucosa    UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 11 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 12 Heart_Left_Ventric… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 13 Lung                UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 14 Prostate            UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(…  # `excludeDataArray = FALSE` - expression values are stored under \"celltypes\" # in an additional column called \"data\" response <- get_single_nucleus_gex(gencodeIds = \"ENSG00000132693.12\",                                    excludeDataArray = FALSE,                                    itemsPerPage = 2) #> Warning: ! Total number of items (7) exceeds maximum page size (2). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 2 #> • totalNumberOfItems = 7  response #> # A tibble: 2 × 7 #>   tissueSiteDetailId   ontologyId datasetId gencodeId geneSymbol cellTypes unit  #>   <chr>                <chr>      <chr>     <chr>     <chr>      <list>    <chr> #> 1 Muscle_Skeletal      UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(… #> 2 Breast_Mammary_Tiss… UBERON:00… gtex_snr… ENSG0000… CRP        <tibble>  log(…  # \"cellTypes\" contains a tibble of data with one row for each # cell type e.g. for Breast_Mammary_Tissue response$cellTypes[[2]] #> # A tibble: 2 × 8 #>   cellType                  count meanWithZeros meanWithoutZeros medianWithZeros #>   <chr>                     <int>         <dbl>            <dbl>           <dbl> #> 1 Epithelial cell (luminal)     2      0.000902             2.19               0 #> 2 Endothelial cell (vascul…     1      0.00401              3.05               0 #> # ℹ 3 more variables: medianWithoutZeros <dbl>, numZeros <int>, data <list>  # when `excludeDataArray = FALSE`, expression values are stored in \"data\" # e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal): response$cellTypes[[2]]$data[[1]] #> [1] 1.593315 2.782725 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"Retrieve Summarized Single Nucleus Gene Expression Data. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"get_single_nucleus_gex_summary(   datasetId = \"gtex_snrnaseq_pilot\",   tissueSiteDetailIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"# \\dontrun{ # all tissues get_single_nucleus_gex_summary() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 114 #> # A tibble: 114 × 5 #>    tissueSiteDetailId ontologyId     datasetId           cellType       numCells #>    <chr>              <chr>          <chr>               <chr>             <int> #>  1 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …      769 #>  2 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (NMJ-…       95 #>  3 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Endothelial c…     1124 #>  4 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. …    20772 #>  5 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Fibroblast         5944 #>  6 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Pericyte/SMC        448 #>  7 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Immune (DC/ma…      721 #>  8 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Adipocyte           159 #>  9 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Schwann cell         35 #> 10 Muscle_Skeletal    UBERON:0011907 gtex_snrnaseq_pilot Satellite cell      487 #> # ℹ 104 more rows  # filter for specific tissue get_single_nucleus_gex_summary(tissueSiteDetailIds = c(\"Breast_Mammary_Tissue\",                                                        \"Skin_Sun_Exposed_Lower_leg\")) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25 #> # A tibble: 25 × 5 #>    tissueSiteDetailId         ontologyId     datasetId         cellType numCells #>    <chr>                      <chr>          <chr>             <chr>       <int> #>  1 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Epithel…     4849 #>  2 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Adipocy…     1761 #>  3 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Immune …      358 #>  4 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Myoepit…      950 #>  5 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Fibrobl…      819 #>  6 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      762 #>  7 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Endothe…      119 #>  8 Breast_Mammary_Tissue      UBERON:0008367 gtex_snrnaseq_pi… Pericyt…      152 #>  9 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Sweat g…      300 #> 10 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Epithel…       72 #> # ℹ 15 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sqtl Genes — get_sqtl_genes","title":"Get Sqtl Genes — get_sqtl_genes","text":"Retrieve sGenes (sQTL Genes). service returns sGenes (sQTL Genes) specified dataset. Results may filtered tissue. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"get_sqtl_genes(   tissueSiteDetailId,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sqtl Genes — get_sqtl_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sqtl Genes — get_sqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"# \\dontrun{ get_sqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (3013) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 13 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3013 #> # A tibble: 250 × 11 #>    nPhenotypes pValueThreshold phenotypeId        geneSymbol    pValue datasetId #>          <int>           <dbl> <chr>              <chr>          <dbl> <chr>     #>  1           9      0.0000145  chr1:15947:16607:… WASH7P     7.15e-  8 gtex_v8   #>  2           6      0.00000634 chr1:1090428:1091… C1orf159   6.85e- 10 gtex_v8   #>  3           7      0.00000908 chr1:1228946:1231… SDF4       1.16e-188 gtex_v8   #>  4           6      0.00000861 chr1:1310688:1310… PUSL1      2.50e- 40 gtex_v8   #>  5           3      0.00000954 chr1:1325102:1327… CPTP       9.60e-  7 gtex_v8   #>  6           2      0.0000147  chr1:1487914:1489… ATAD3C     1.61e- 25 gtex_v8   #>  7           5      0.00000740 chr1:1487914:1489… ATAD3B     1.61e- 25 gtex_v8   #>  8           2      0.0000361  chr1:1545002:1547… SSU72      3.28e- 25 gtex_v8   #>  9          19      0.00000176 chr1:1629311:1629… MIB2       1.97e- 12 gtex_v8   #> 10           8      0.00000273 chr1:1641113:1641… CDK11B     3.08e- 56 gtex_v8   #> # ℹ 240 more rows #> # ℹ 5 more variables: empiricalPValue <dbl>, tissueSiteDetailId <chr>, #> #   ontologyId <chr>, qValue <dbl>, gencodeId <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Subject — get_subject","title":"Get Subject — get_subject","text":"service returns information subjects used analyses datasets. Results may filtered dataset ID, subject ID, sex, age bracket Hardy Scale. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Subject — get_subject","text":"","code":"get_subject(   datasetId = \"gtex_v8\",   sex = NULL,   ageBrackets = NULL,   hardyScales = NULL,   subjectIds = NULL,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Subject — get_subject","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sex String. Options: \"male\", \"female\". ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". subjectIds Character vector. GTEx subject ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Subject — get_subject","text":"Tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Subject — get_subject","text":"","code":"# \\dontrun{   get_subject() #> Warning: ! Total number of items (979) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 979 #> # A tibble: 250 × 5 #>    hardyScale                  ageBracket subjectId  sex    datasetId #>    <chr>                       <chr>      <chr>      <chr>  <chr>     #>  1 Slow death                  60-69      GTEX-1117F female gtex_v8   #>  2 Ventilator case             50-59      GTEX-111CU male   gtex_v8   #>  3 Fast death - violent        60-69      GTEX-111FC male   gtex_v8   #>  4 Intermediate death          60-69      GTEX-111VG male   gtex_v8   #>  5 Ventilator case             60-69      GTEX-111YS male   gtex_v8   #>  6 Ventilator case             60-69      GTEX-1122O female gtex_v8   #>  7 Fast death - natural causes 60-69      GTEX-1128S female gtex_v8   #>  8 NA                          60-69      GTEX-113IC male   gtex_v8   #>  9 Fast death - natural causes 50-59      GTEX-113JC female gtex_v8   #> 10 Fast death - natural causes 60-69      GTEX-117XS male   gtex_v8   #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Tissue Site Detail — get_tissue_site_detail","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"Retrieve tissue site detail information database GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"get_tissue_site_detail(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"# \\dontrun{   # returns a tibble with one row per tissue   get_tissue_site_detail() #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 18 #>    tissueSiteDetailId  colorHex colorRgb datasetId eGeneCount expressedGeneCount #>    <chr>               <chr>    <chr>    <chr>          <int>              <int> #>  1 Adipose_Subcutaneo… FF6600   255,102… gtex_v8        15607              28830 #>  2 Adipose_Visceral_O… FFAA00   255,170… gtex_v8        12482              28881 #>  3 Adrenal_Gland       33DD33   51,221,… gtex_v8         8123              28235 #>  4 Artery_Aorta        FF5555   255,85,… gtex_v8        12493              28025 #>  5 Artery_Coronary     FFAA99   255,170… gtex_v8         6296              28462 #>  6 Artery_Tibial       FF0000   255,0,0  gtex_v8        15008              27217 #>  7 Bladder             AA0000   170,0,0  gtex_v8           NA              28949 #>  8 Brain_Amygdala      EEEE00   238,238… gtex_v8         3726              28196 #>  9 Brain_Anterior_cin… EEEE00   238,238… gtex_v8         5640              28921 #> 10 Brain_Caudate_basa… EEEE00   238,238… gtex_v8         8362              29230 #> # ℹ 44 more rows #> # ℹ 12 more variables: hasEGenes <lgl>, hasSGenes <lgl>, mappedInHubmap <lgl>, #> #   eqtlSampleSummary <list>, rnaSeqSampleSummary <list>, sGeneCount <int>, #> #   samplingSite <chr>, tissueSite <chr>, tissueSiteDetail <chr>, #> #   tissueSiteDetailAbbr <chr>, ontologyId <chr>, ontologyIri <chr>    # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns   bladder_site_details <- get_tissue_site_detail() |>     dplyr::filter(tissueSiteDetailId == \"Bladder\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54    purrr::pluck(bladder_site_details, \"eqtlSampleSummary\", 1) #> $totalCount #> [1] 21 #>  #> $female #> $female$ageMax #> [1] 59 #>  #> $female$ageMin #> [1] 27 #>  #> $female$ageMean #> [1] 43.6 #>  #> $female$count #> [1] 7 #>  #>  #> $male #> $male$ageMax #> [1] 61 #>  #> $male$ageMin #> [1] 21 #>  #> $male$ageMean #> [1] 46 #>  #> $male$count #> [1] 14 #>  #>     purrr::pluck(bladder_site_details, \"rnaSeqSampleSummary\", 1) #> $totalCount #> [1] 21 #>  #> $female #> $female$ageMax #> [1] 59 #>  #> $female$ageMin #> [1] 27 #>  #> $female$ageMean #> [1] 43.6 #>  #> $female$count #> [1] 7 #>  #>  #> $male #> $male$ageMax #> [1] 61 #>  #> $male$ageMin #> [1] 21 #>  #> $male$ageMean #> [1] 46 #>  #> $male$count #> [1] 14 #>  #>  # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Top Expressed Genes — get_top_expressed_genes","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"Find top expressed genes specified tissue. Returns top expressed genes specified tissue dataset, sorted median expression. optional parameter filterMtGene set true, mitochondrial genes excluded results. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"get_top_expressed_genes(   tissueSiteDetailId,   datasetId = \"gtex_v8\",   filterMtGene = TRUE,   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". filterMtGene Logical. Exclude mitochondrial genes. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"# \\dontrun{ get_top_expressed_genes(tissueSiteDetailId = \"Artery_Aorta\") #> Warning: ! Total number of items (56163) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 225 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 56163 #> # A tibble: 250 × 7 #>    tissueSiteDetailId ontologyId     datasetId gencodeId geneSymbol median unit  #>    <chr>              <chr>          <chr>     <chr>     <chr>       <dbl> <chr> #>  1 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MGP        11936. TPM   #>  2 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FTL         9196. TPM   #>  3 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTB        9154. TPM   #>  4 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… BGN         8167. TPM   #>  5 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… TAGLN       6099. TPM   #>  6 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTA2       5736. TPM   #>  7 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… IGFBP7      5639. TPM   #>  8 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MYL9        4275. TPM   #>  9 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… HSPB1       3780. TPM   #> 10 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FLNA        3732. TPM   #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Transcripts — get_transcripts","title":"Get Transcripts — get_transcripts","text":"Find transcripts reference gene. service returns information transcripts given versioned GENCODE ID. genome build GENCODE version must provided. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Transcripts — get_transcripts","text":"","code":"get_transcripts(   gencodeId,   gencodeVersion = \"v26\",   genomeBuild = \"GRCh38/hg38\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Transcripts — get_transcripts","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Transcripts — get_transcripts","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Transcripts — get_transcripts","text":"","code":"# \\dontrun{ get_transcripts(gencodeId = \"ENSG00000203782.5\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 11 #>    start    end featureType genomeBuild transcriptId source chromosome gencodeId #>    <int>  <int> <chr>       <chr>       <chr>        <chr>  <chr>      <chr>     #> 1 1.53e8 1.53e8 transcript  GRCh38/hg38 ENST0000036… HAVANA chr1       ENSG0000… #> # ℹ 3 more variables: geneSymbol <chr>, gencodeVersion <chr>, strand <chr> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant — get_variant","title":"Get Variant — get_variant","text":"service returns information variant, including position, dbSNP RS ID, reference allele, alternative allele, whether minor allele frequency >= 1%. GTEx v6p, also information whether whole exome sequence chip sequencing data available. Results may queried GTEx variant ID (variantId), dbSNP RS ID (snpId) genomic location (chromosome pos). Variants identified based genotype data dataset cohort, namely, dataset-dependent. variant assigned unique GTEx variant ID (.e. primary key). variants mappable dbSNP RS ID. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant — get_variant","text":"","code":"get_variant(   snpId = NULL,   variantId = NULL,   chromosome = NULL,   pos = NULL,   datasetId = \"gtex_v8\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant — get_variant","text":"snpId String variantId String. gtex variant ID. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". pos Integer, vector. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant — get_variant","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant — get_variant","text":"","code":"# search by rsid get_variant(snpId = \"rs1410858\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #>   snpId     b37VariantId         pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>     <chr>              <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> # ℹ 2 more variables: datasetId <chr>, ref <chr>  # search by variantId get_variant(variantId = \"chr1_153209640_C_A_b38\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #>   snpId     b37VariantId         pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>     <chr>              <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> # ℹ 2 more variables: datasetId <chr>, ref <chr>  # search by chromosome and position get_variant(chromosome = \"chr1\",             pos = 153209600:153209700) #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #>   snpId       b37VariantId       pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>       <chr>            <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs11205220  1_153182115_T_… 1.53e8 TRUE  chr1_153… C     chr1       RS11205220 #> 2 rs1410858   1_153182116_C_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T     chr1       RS1392967… #> 4 rs80104092  1_153182149_T_… 1.53e8 FALSE chr1_153… C     chr1       RS80104092 #> # ℹ 2 more variables: datasetId <chr>, ref <chr>"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant By Location — get_variant_by_location","title":"Get Variant By Location — get_variant_by_location","text":"service allows user query information variants certain chromosome certain location. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(   start,   end,   chromosome,   sortBy = \"pos\",   sortDirection = \"asc\",   page = 0,   itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant By Location — get_variant_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant By Location — get_variant_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(start = 153209600,                         end = 153209700,                         chromosome = \"chr1\") #>  #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #>   snpId       b37VariantId       pos maf01 variantId alt   chromosome snpIdUpper #>   <chr>       <chr>            <int> <lgl> <chr>     <chr> <chr>      <chr>      #> 1 rs11205220  1_153182115_T_… 1.53e8 TRUE  chr1_153… C     chr1       RS11205220 #> 2 rs1410858   1_153182116_C_… 1.53e8 TRUE  chr1_153… A     chr1       RS1410858  #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T     chr1       RS1392967… #> 4 rs80104092  1_153182149_T_… 1.53e8 FALSE chr1_153… C     chr1       RS80104092 #> # ℹ 2 more variables: datasetId <chr>, ref <chr>"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr: Query the GTEx Portal API — gtexr-package","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"convenient R interface Genotype-Tissue Expression (GTEx) Portal API. information API, see https://gtexportal.org/api/v2/redoc.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"Maintainer: Alasdair Warwick alasdair.warwick.19@ucl.ac.uk (ORCID) [copyright holder] Authors: Benjamin Zuckerman (ORCID) Abraham Olvera-Barrios (ORCID) Chuin Ying Ung (ORCID) Robert Luben (ORCID)","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr arguments — gtexr_arguments","title":"gtexr arguments — gtexr_arguments","text":"Internal function documents arguments exported gtexr functions wrap GTEx Portal API endpoints (using roxygen @inheritParams tag).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gtexr arguments — gtexr_arguments","text":"","code":"gtexr_arguments(   ageBrackets = NULL,   aliquotIds = NULL,   attributeSubset = NULL,   autolysisScores = NULL,   cellType = NULL,   bp_window = NULL,   chromosome = NULL,   datasetId = NULL,   dataTypes = NULL,   draw = NULL,   end = NULL,   excludeDataArray = NULL,   .featureId = NULL,   filterMtGene = NULL,   gencodeId = NULL,   gencodeIds = NULL,   gencodeVersion = NULL,   geneId = NULL,   geneIds = NULL,   genomeBuild = NULL,   hardyScales = NULL,   hasExpressionData = NULL,   hasGenotype = NULL,   itemsPerPage = NULL,   ischemicTime = NULL,   ischemicTimeGroups = NULL,   materialTypes = NULL,   organizationName = NULL,   page = NULL,   pathCategory = NULL,   phenotypeId = NULL,   pos = NULL,   project_id = NULL,   rin = NULL,   sampleId = NULL,   sampleIds = NULL,   searchTerm = NULL,   sex = NULL,   snpId = NULL,   sortBy = NULL,   sortDirection = NULL,   start = NULL,   subjectIds = NULL,   tissueSampleIds = NULL,   tissueSiteDetailId = NULL,   tissueSiteDetailIds = NULL,   uberonIds = NULL,   variantId = NULL,   variantIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gtexr arguments — gtexr_arguments","text":"ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". aliquotIds Character vector. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". bp_window Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". draw Integer. end Integer. excludeDataArray String. Options TRUE FALSE .featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. filterMtGene Logical. Exclude mitochondrial genes. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". geneId String. gene symbol, gencode ID, Ensemble ID. geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. itemsPerPage Integer (default = 250). ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\". page Integer (default = 0). pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". phenotypeId String. See GTEx portal FAQs details. pos Integer, vector. project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\". rin Integer vector. sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ sampleIds Character vector. GTEx sample ID. searchTerm String. sex String. Options: \"male\", \"female\". snpId String sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". start Integer. subjectIds Character vector. GTEx subject ID. tissueSampleIds Array strings. list Tissue Sample ID(s). tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). variantId String. gtex variant ID. variantIds Character vector. Gtex variant IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gtexr arguments — gtexr_arguments","text":"Returns NULL invisibly. Used documentation .","code":""},{"path":"https://rmgpanw.github.io/gtexr/news/index.html","id":"gtexr-010","dir":"Changelog","previous_headings":"","what":"gtexr 0.1.0","title":"gtexr 0.1.0","text":"CRAN release: 2024-09-19 Initial CRAN submission.","code":""}]