From 3209fea6e88839bb778455f133fe4b11ce2b5490 Mon Sep 17 00:00:00 2001
From: Ed2uiz <32622519+Ed2uiz@users.noreply.github.com>
Date: Wed, 18 Sep 2024 15:28:23 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20drieslab?=
 =?UTF-8?q?/dbMatrix@2c41e968c37cc7fa7f9c217e588b00cdbac3e159=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                   |  2 +-
 GPL-3.html                                 |  2 +-
 LICENSE-text.html                          |  2 +-
 articles/arithmetic.html                   |  6 ++--
 articles/index.html                        |  2 +-
 articles/operations.html                   |  6 ++--
 articles/overview.html                     |  2 +-
 authors.html                               |  6 ++--
 index.html                                 |  2 +-
 news/index.html                            | 39 +++++++++++++++++++++-
 pkgdown.yml                                |  2 +-
 reference/as.matrix-dbMatrix-method.html   |  2 +-
 reference/dbList-DBIConnection-method.html |  2 +-
 reference/dbMatrix.html                    |  2 +-
 reference/dbMatrix_from_tbl.html           |  2 +-
 reference/dim-dbMatrix-method.html         |  2 +-
 reference/dot-check_con.html               |  2 +-
 reference/dot-check_name.html              |  2 +-
 reference/dot-check_overwrite.html         |  2 +-
 reference/dot-check_value.html             |  2 +-
 reference/get_MM_dim.html                  |  2 +-
 reference/get_MM_dimnames.html             |  2 +-
 reference/get_con.html                     |  2 +-
 reference/get_dbdir.html                   |  2 +-
 reference/get_tblName.html                 |  2 +-
 reference/head_tail.html                   |  2 +-
 reference/index.html                       |  2 +-
 reference/log-dbMatrix-method.html         |  2 +-
 reference/map_ijx_dimnames.html            |  2 +-
 reference/matrix_props.html                |  2 +-
 reference/mean.html                        |  2 +-
 reference/nrow_ncol.html                   |  2 +-
 reference/precompute.html                  |  2 +-
 reference/print_array.html                 |  2 +-
 reference/row_col_means.html               |  2 +-
 reference/row_col_sums.html                |  2 +-
 reference/sds.html                         |  2 +-
 reference/simulate_objects.html            |  2 +-
 reference/sum-dbMatrix-method.html         |  2 +-
 reference/t-dbMatrix-method.html           |  2 +-
 reference/to_ijx_disk.html                 |  2 +-
 search.json                                |  2 +-
 42 files changed, 85 insertions(+), 48 deletions(-)

diff --git a/404.html b/404.html
index 8bc0404..18399a8 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://drieslab.github.io/dbMatrix/index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/GPL-3.html b/GPL-3.html
index cddca32..e57636b 100644
--- a/GPL-3.html
+++ b/GPL-3.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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 c69f781..f6a5d61 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/arithmetic.html b/articles/arithmetic.html
index 63c089a..ea9606c 100644
--- a/articles/arithmetic.html
+++ b/articles/arithmetic.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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">
@@ -239,7 +239,7 @@ <h3 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; R version 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">#&gt; Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">#&gt; Running under: Ubuntu 22.04.5 LTS</span></span>
+<span><span class="co">#&gt; Running under: Ubuntu 22.04.4 LTS</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Matrix products: default</span></span>
 <span><span class="co">#&gt; BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
@@ -258,7 +258,7 @@ <h3 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] Matrix_1.7-0        dbMatrix_0.0.0.9022</span></span>
+<span><span class="co">#&gt; [1] Matrix_1.7-0        dbMatrix_0.0.0.9023</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;  [1] bit_4.0.5             jsonlite_1.8.8        crayon_1.5.3         </span></span>
diff --git a/articles/index.html b/articles/index.html
index 6d6f045..ed174b2 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/operations.html b/articles/operations.html
index a33728c..926917f 100644
--- a/articles/operations.html
+++ b/articles/operations.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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">
@@ -461,7 +461,7 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## R version 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">## Running under: Ubuntu 22.04.5 LTS</span></span>
+<span><span class="co">## Running under: Ubuntu 22.04.4 LTS</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Matrix products: default</span></span>
 <span><span class="co">## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
@@ -481,7 +481,7 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] Matrix_1.7-0        dbMatrix_0.0.0.9022</span></span>
+<span><span class="co">## [1] Matrix_1.7-0        dbMatrix_0.0.0.9023</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
 <span><span class="co">##  [1] jsonlite_1.8.8    crayon_1.5.3      dplyr_1.1.4       compiler_4.4.1   </span></span>
diff --git a/articles/overview.html b/articles/overview.html
index 5057a52..1bd07e4 100644
--- a/articles/overview.html
+++ b/articles/overview.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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 da260a9..f0680ab 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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">
@@ -66,13 +66,13 @@ <h2 id="citation">Citation</h2>
 
       <p>C. Ruiz E, George Chen J, Dries R (2024).
 <em>dbMatrix: dbMatrix</em>.
-R package version 0.0.0.9022, <a href="https://drieslab.github.io/dbMatrix/">https://drieslab.github.io/dbMatrix/</a>.
+R package version 0.0.0.9023, <a href="https://drieslab.github.io/dbMatrix/">https://drieslab.github.io/dbMatrix/</a>.
 </p>
       <pre>@Manual{,
   title = {dbMatrix: dbMatrix},
   author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries},
   year = {2024},
-  note = {R package version 0.0.0.9022},
+  note = {R package version 0.0.0.9023},
   url = {https://drieslab.github.io/dbMatrix/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 337a229..2baeb9f 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/news/index.html b/news/index.html
index 18e55dd..d21107b 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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">
@@ -44,6 +44,43 @@ <h1>Changelog</h1>
       <small>Source: <a href="https://github.com/drieslab/dbMatrix/blob/dev/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.0.0.9023" id="dbmatrix-0009023-2024-09-18">dbMatrix 0.0.0.9023 (2024-09-18)<a class="anchor" aria-label="anchor" href="#dbmatrix-0009023-2024-09-18"></a></h2>
+<div class="section level3">
+<h3 id="breaking-changes-0-0-0-9023">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-0-0-0-9023"></a></h3>
+<ul><li><p>dbMatrix summary methods now return <code>dbDenseMatrix</code> objects instead of in-memory vectors.</p></li>
+<li><p>Removed colTypes from castNumeric.</p></li>
+<li><p>Removed <a href="https://github.com/name" class="external-link">@name</a> check in initialize.</p></li>
+</ul></div>
+<div class="section level3">
+<h3 id="features-0-0-0-9023">Features<a class="anchor" aria-label="anchor" href="#features-0-0-0-9023"></a></h3>
+<ul><li><p>New <code>compute</code> method for saving dbMatrix objects. This writes the dbMatrix object to a table in the database along with its row and column names (e.g. ‘dbMatrixname_rownames’).</p></li>
+<li><p>New <code>load</code> method for loading computed dbMatrix objects. The dbMatrix::compute() method must be called before loading the object.</p></li>
+<li><p>Updated <code>.check_overwrite</code> to allow for passing overwrite arg.</p></li>
+<li><p>New internal function <code>write_dimnames</code> to enable saving dbMatrix objects.</p></li>
+<li><p>New <code>sum</code> method for dbMatrix objects.</p></li>
+<li><p>Improvements to precomputed table: Use existing precomputed table in db if available.</p></li>
+<li><p>Improvements to precomputed table: Transpose precomputed table of sufficient dimensions if it exists instead of creating a new one. This is done via a TEMPORARY VIEW to avoid writing to disk and modifying existing precomputed table which may be referenced by other tables.</p></li>
+<li><p>Custom SQL statement for <code>todbDense</code> conversion creates a TEMPORARY VIEW with name <code>dbDenseMatrix_hash</code>.</p></li>
+</ul></div>
+<div class="section level3">
+<h3 id="chore-0-0-0-9023">Chore<a class="anchor" aria-label="anchor" href="#chore-0-0-0-9023"></a></h3>
+<ul><li><p>Update whitespace.</p></li>
+<li><p>Update dbMatrix constructor roxygen.</p></li>
+<li><p>Update roxygen in toDbDense.</p></li>
+</ul></div>
+<div class="section level3">
+<h3 id="docs-0-0-0-9023">Docs<a class="anchor" aria-label="anchor" href="#docs-0-0-0-9023"></a></h3>
+<ul><li><p>Update reference page.</p></li>
+<li><p>Update mean documentation.</p></li>
+<li><p>Update log documentation.</p></li>
+<li><p>Update roxygen.</p></li>
+</ul></div>
+<div class="section level3">
+<h3 id="bug-fixes-0-0-0-9023">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-0-0-9023"></a></h3>
+<ul><li>Do not recycle matrix if not needed.</li>
+</ul></div>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.0.9022" id="dbmatrix-0009022-2024-08-14">dbMatrix 0.0.0.9022 (2024-08-14)<a class="anchor" aria-label="anchor" href="#dbmatrix-0009022-2024-08-14"></a></h2>
 <div class="section level3">
diff --git a/pkgdown.yml b/pkgdown.yml
index 99d7a14..8d28582 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   arithmetic: arithmetic.html
   operations: operations.html
   overview: overview.html
-last_built: 2024-09-18T15:12Z
+last_built: 2024-09-18T15:28Z
 urls:
   reference: https://drieslab.github.io/dbMatrix/reference
   article: https://drieslab.github.io/dbMatrix/articles
diff --git a/reference/as.matrix-dbMatrix-method.html b/reference/as.matrix-dbMatrix-method.html
index 9f09749..8db4e57 100644
--- a/reference/as.matrix-dbMatrix-method.html
+++ b/reference/as.matrix-dbMatrix-method.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dbList-DBIConnection-method.html b/reference/dbList-DBIConnection-method.html
index 9660afd..bbe82f3 100644
--- a/reference/dbList-DBIConnection-method.html
+++ b/reference/dbList-DBIConnection-method.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dbMatrix.html b/reference/dbMatrix.html
index fc79974..d7c387a 100644
--- a/reference/dbMatrix.html
+++ b/reference/dbMatrix.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dbMatrix_from_tbl.html b/reference/dbMatrix_from_tbl.html
index e63ca72..78fbebc 100644
--- a/reference/dbMatrix_from_tbl.html
+++ b/reference/dbMatrix_from_tbl.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dim-dbMatrix-method.html b/reference/dim-dbMatrix-method.html
index 151a1d7..7876969 100644
--- a/reference/dim-dbMatrix-method.html
+++ b/reference/dim-dbMatrix-method.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dot-check_con.html b/reference/dot-check_con.html
index cd2dcea..02ef794 100644
--- a/reference/dot-check_con.html
+++ b/reference/dot-check_con.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dot-check_name.html b/reference/dot-check_name.html
index 37c06c5..fb78641 100644
--- a/reference/dot-check_name.html
+++ b/reference/dot-check_name.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">dbMatrix</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9022</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9023</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/dot-check_overwrite.html b/reference/dot-check_overwrite.html
index 0cb6c23..bbfbc93 100644
--- a/reference/dot-check_overwrite.html
+++ b/reference/dot-check_overwrite.html
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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Note: operations zero values yet supported dbMatrix objects. addition, certain arithmetic operations dbMatrix objects also yet supported. welcome user feedback reporting issues Github page.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) #> Loading required package: Matrix #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #>   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #>   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #>   ..@ Dim     : int [1:2] 634 624 #>   ..@ Dimnames:List of 2 #>   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #>   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #>   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #>   ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\")  dbsm <- dbMatrix(value = dgc,                   con = con,                   name = 'visium',                   class = \"dbSparseMatrix\",                  overwrite = TRUE)  # preview the object dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> ℹ Densifying 'dbSparseMatrix' on the fly... #> 634 x 624  matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                    #> Gna12         2 3 2 2 10 2 4 6 4 1 #> Ccnd2         1 2 2 1  1 2 1 2 2 1 #> Btbd17        1 2 2 2  1 1 3 1 1 1 #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       1 2 1 1  1 1 1 1 1 1 #> 9630013A20Rik 1 1 1 1  1 1 1 1 1 1 #> 2900040C04Rik 2 1 1 1  1 1 1 1 1 2  dbsm * 100 #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                                       #> Gna12         100 200 100 100 900 100 300 500 300   . #> Ccnd2           . 100 100   .   . 100   . 100 100   . #> Btbd17          . 100 100 100   .   . 200   .   .   . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935         . 100   .   .   .   .   .   .   .   . #> 9630013A20Rik   .   .   .   .   .   .   .   .   .   . #> 2900040C04Rik 100   .   .   .   .   .   .   .   . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         2 4 2 2 18 2 6 10 6 . #> Ccnd2         . 2 2 .  . 2 .  2 2 . #> Btbd17        . 2 2 2  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 2 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 2 . . .  . . .  . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"dbMatrix arithmetic > Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         1 4 1 1 81 1 9 25 9 . #> Ccnd2         . 1 1 .  . 1 .  1 1 . #> Btbd17        . 1 1 1  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 1 . . .  . . .  . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"dbMatrix arithmetic > Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] Matrix_1.7-0        dbMatrix_0.0.0.9022 #>  #> loaded via a namespace (and not attached): #>  [1] bit_4.0.5             jsonlite_1.8.8        crayon_1.5.3          #>  [4] dplyr_1.1.4           compiler_4.4.1        tidyselect_1.2.1      #>  [7] blob_1.2.4            jquerylib_0.1.4       systemfonts_1.1.0     #> [10] textshaping_0.4.0     yaml_2.3.10           fastmap_1.2.0         #> [13] lattice_0.22-6        R6_2.5.1              generics_0.1.3        #> [16] knitr_1.48            tibble_3.2.1          desc_1.4.3            #> [19] MatrixGenerics_1.16.0 DBI_1.2.3             bslib_0.8.0           #> [22] pillar_1.9.0          rlang_1.1.4           utf8_1.2.4            #> [25] cachem_1.1.0          xfun_0.47             fs_1.6.4              #> [28] sass_0.4.9            bit64_4.0.5           cli_3.6.3             #> [31] withr_3.0.1           pkgdown_2.1.1         magrittr_2.0.3        #> [34] digest_0.6.37         grid_4.4.1            dbplyr_2.5.0          #> [37] lifecycle_1.0.4       vctrs_0.6.5           evaluate_1.0.0        #> [40] glue_1.7.0            data.table_1.16.0     duckdb_1.0.0-2        #> [43] ragg_1.3.3            fansi_1.0.6           purrr_1.0.2           #> [46] rmarkdown_2.28        matrixStats_1.4.1     tools_4.4.1           #> [49] pkgconfig_2.0.3       htmltools_0.5.8.1"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix objects currently support several statistical matrix operations listed support coming soon. ✅ - implemented 🟧 - yet implemented","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ##   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ##   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ##   ..@ Dim     : int [1:2] 634 624 ##   ..@ Dimnames:List of 2 ##   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ##   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ##   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ##   ..@ factors : list() # create dbSparseMatrix from the same dgc con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\")  sparse <- dbMatrix(value = dgc,                     con = con,                     name = 'visium',                     class = \"dbSparseMatrix\",                    overwrite = TRUE)  # preview  # show function aims to emulate the show method for dgCMatrix head(sparse) ## 6 x 624  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                   ## Gna12         1 2 1 1 9 1 3 5 3 . ##  [ reached getOption(\"max.print\") -- omitted 633 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## 624 x 634  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ##                                        ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ##  ## ......suppressing 624 columns and 618 rows ##  ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## 1 x 624  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                                                             ## row1 0.74132 1.32965 1.14353 0.83438 1.61356 2.21293 1.7224 1.90221 0.73975 ##              ## row1 0.92587"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## 1 x 624  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                                  ## row1 470 843 725 529 1023 1403 1092 1206 469 587"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ## 634 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                       ## Gna12         2.71795 ## Ccnd2         1.73237 ## Btbd17        0.55288 ##  ## ......suppressing 628 rows ##  ## Gm19935       0.20833 ## 9630013A20Rik 0.17147 ## 2900040C04Rik 0.15545"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ## 634 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                    ## Gna12         1696 ## Ccnd2         1081 ## Btbd17         345 ##  ## ......suppressing 628 rows ##  ## Gm19935        130 ## 9630013A20Rik  107 ## 2900040C04Rik   97"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 624\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 624\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 634\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 634\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix()  # preview dense ## 50 x 50  matrix of class \"dbDenseMatrix\" ##                                                                               ## row1   1.37096  0.32193  1.20097  -0.0407 -2.00093 -1.09616 -0.00462  0.72417 ##                         ## row1   1.33491 -1.30382 ##  ## ......suppressing 40 columns and 44 rows ##  ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## 50 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ##                                                                               ## col1   1.37096  -0.5647  0.36313  0.63286  0.40427 -0.10612  1.51152 -0.09466 ##                         ## col1   2.01842 -0.06271 ##  ## ......suppressing 40 columns and 44 rows ##  ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ## 1 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'col1', 'col2', 'col3' ... suppressing 44 ...'col48', 'col49', 'col50' ]] ##                                                                           ## row1 -0.03562 0.10074 -0.15122 -0.02372 0.00794 -0.02862 -0.06156 0.12742 ##                        ## row1 -0.11944 -0.11622"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ## 1 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'col1', 'col2', 'col3' ... suppressing 44 ...'col48', 'col49', 'col50' ]] ## Warning: ORDER BY is ignored in subqueries without LIMIT ## ℹ Do you need to move arrange() later in the pipeline or use window_order() instead? ##                                                                         ## row1 -1.781 5.037 -7.561 -1.186 0.397 -1.431 -3.078 6.371 -5.972 -5.811"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ## 50 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                ## row1   0.05362 ## row2   0.00246 ## row3   0.03132 ##  ## ......suppressing 44 rows ##  ## row48 -0.10104 ## row49  0.05928 ## row50  0.02156"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ## 50 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ## Warning: ORDER BY is ignored in subqueries without LIMIT ## ℹ Do you need to move arrange() later in the pipeline or use window_order() instead? ##              ## row1   2.681 ## row2   0.123 ## row3   1.566 ##  ## ......suppressing 44 rows ##  ## row48 -5.052 ## row49  2.964 ## row50  1.078"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.0096724"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8    LC_NUMERIC=C        LC_TIME=C.UTF-8     ##  [4] LC_COLLATE=C.UTF-8  LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ##  [7] LC_PAPER=C.UTF-8    LC_NAME=C           LC_ADDRESS=C        ## [10] LC_TELEPHONE=C      ##  [ reached getOption(\"max.print\") -- omitted 2 entries ] ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] Matrix_1.7-0        dbMatrix_0.0.0.9022 ##  ## loaded via a namespace (and not attached): ##  [1] jsonlite_1.8.8    crayon_1.5.3      dplyr_1.1.4       compiler_4.4.1    ##  [5] tidyselect_1.2.1  blob_1.2.4        jquerylib_0.1.4   systemfonts_1.1.0 ##  [9] textshaping_0.4.0 yaml_2.3.10       ##  [ reached getOption(\"max.print\") -- omitted 38 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author, maintainer. Jiaji George Chen. Author. Ruben Dries. Author.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9022, https://drieslab.github.io/dbMatrix/.","code":"@Manual{,   title = {dbMatrix: dbMatrix},   author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries},   year = {2024},   note = {R package version 0.0.0.9022},   url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations. Note: Work progress! Bugs unexpected behavior likely occur. welcome user feedback reporting issues Github page.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"Converts dbMatrix object -memory matrix sparse matrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' as.matrix(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"x dbMatrix object (dbSparseMatrix dbDenseMatrix) ... Additional arguments (used)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"Matrix::dgCMatrix base R matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"method converts dbMatrix object (dbSparseMatrix dbDenseMatrix) -memory Matrix::dgCMatrix (sparse) base R matrix (dense). Warning: can cause memory issues input matrix large.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":null,"dir":"Reference","previous_headings":"","what":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"Pretty prints tables, temporary tables, views database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"","code":"# S4 method for class 'DBIConnection' dbList(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"conn DBIConnection object, returned dbConnect().","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"Similar DBI::dbListTables, categorizes tables three categories: Tables Temporary Tables (removed connection closed) Views (may removed connection closed)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"","code":"dbMatrix(   value,   class = NULL,   con = NULL,   overwrite = FALSE,   name = \"dbMatrix\",   dims = NULL,   dim_names = NULL,   mtx_rowname_file_path,   mtx_rowname_col_idx = 1,   mtx_colname_file_path,   mtx_colname_col_idx = 1,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) con DBI duckdb connection object (required) overwrite whether overwrite table already exists database (required) name table name assign within database (required, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) mtx_rowname_file_path path .mtx rowname file read (optional) database. default, header assumed. mtx_rowname_col_idx column index row name file (optional) mtx_colname_file_path path .mtx colname file read database. default, header assumed. (optional) mtx_colname_col_idx column index column name file (optional) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"function reads data pre-existing DuckDB database. Supported value data types: dgCMatrix -memory sparse matrix Matrix package dgTMatrix -memory triplet vector COO matrix matrix -memory dense matrix base R .mtx Path .mtx file .csv Path .csv file tbl_duckdb_connection Table DuckDB database ijx format existing dbMatrix object. dims dim_names must specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"","code":"dgc = readRDS(system.file(\"data\", \"dgc.rds\", package = \"dbMatrix\")) #> Loading required package: Matrix con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") dbSparse <- dbMatrix(   value = dgc,   con = con,   name = \"sparse_matrix\",   class = \"dbSparseMatrix\",   overwrite = TRUE ) dbSparse #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"dbMatrix_from_tbl — dbMatrix_from_tbl","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"Construcst dbSparseMatrix object tbl_duckdb_connection object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"","code":"dbMatrix_from_tbl(   tbl,   rownames_colName,   colnames_colName,   name = \"dbMatrix\",   overwrite = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"tbl tbl_duckdb_connection table DuckDB database long format rownames_colName character column name rownames tbl (required) colnames_colName character column name colnames tbl (required) name table name assign within database (required, default: \"dbMatrix\") overwrite whether overwrite table already exists database (required) con DBI duckdb connection object (required)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"tbl_duckdb_connection object must contain dimension names.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimensions of an Object — dim,dbMatrix-method","title":"Dimensions of an Object — dim,dbMatrix-method","text":"Retrieve dimension object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimensions of an Object — dim,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimensions of an Object — dim,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for conn arg — .check_con","title":"Input validation for conn arg — .check_con","text":"Input validation conn arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for conn arg — .check_con","text":"","code":".check_con(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for conn arg — .check_con","text":"conn tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for name arg — .check_name","title":"Input validation for name arg — .check_name","text":"Input validation name arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for name arg — .check_name","text":"","code":".check_name(name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for overwrite arg — .check_overwrite","title":"Input validation for overwrite arg — .check_overwrite","text":"Input validation overwrite arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for overwrite arg — .check_overwrite","text":"","code":".check_overwrite(conn, overwrite, name, skip_value_check = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for data arg — .check_value","title":"Input validation for data arg — .check_value","text":"Input validation data arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for data arg — .check_value","text":"","code":".check_value(value)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for data arg — .check_value","text":"x Matrix, matrix, tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dim — get_MM_dim","title":"get_MM_dim — get_MM_dim","text":"Internal function read dimensions .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dim — get_MM_dim","text":"","code":"get_MM_dim(mtx_file_path)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dim — get_MM_dim","text":"mtx_file_path path .mtx file read database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dim — get_MM_dim","text":"integer vector dimensions","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dim — get_MM_dim","text":"Scans header mtx file (starting %) takes one line representing dimensions number nonzero values. Note: header size can vary depending .mtx file.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dimnames — get_MM_dimnames","title":"get_MM_dimnames — get_MM_dimnames","text":"Internal function read row column names .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dimnames — get_MM_dimnames","text":"","code":"get_MM_dimnames(   mtx_file_path,   mtx_rowname_file_path,   mtx_rowname_col_idx = 1,   mtx_colname_file_path,   mtx_colname_col_idx = 1,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dimnames — get_MM_dimnames","text":"mtx_file_path path .mtx file read database mtx_rowname_file_path path .mtx rowname file read database. default, header assumed. mtx_rowname_col_idx column index row name file mtx_colname_file_path path .mtx colname file read database. default, header assumed. mtx_colname_col_idx column index column name file ... additional params pass data.table::fread","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dimnames — get_MM_dimnames","text":"list row column name character vectors","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dimnames — get_MM_dimnames","text":"Can used read row column names .mtx files. Note: files must contain header (colnames). mtx_rowname_col_idx mtx_colname_col_idx can used specify column index row column name files, respectively. default, first column used . TODO: Support reading rownames colnames.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the First or Last Parts of an Object — head,dbMatrix-method","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"Returns first last parts vector, matrix, table, data frame   function.  Since head() tail() generic   functions, may also extended classes.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' head(x, n = 6L, ...)  # S4 method for class 'dbMatrix' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"x object n integer vector length dim(x) (1,     non-dimensioned objects).  logical silently coerced     integer.  Values specify indices     selected corresponding dimension (along length)     object. positive value n[] includes first/last     n[] indices dimension, negative value     excludes last/first abs(n[]), including remaining     indices. NA non-specified values (length(n) <       length(dim(x))) select indices dimension. Must     contain least one non-missing value. ... arguments passed methods.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Logarithms and Exponentials — log,dbMatrix-method","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"log computes logarithms, default natural logarithms,   log10 computes common (.e., base 10) logarithms,   log2 computes binary (.e., base 2) logarithms.   general form log(x, base) computes logarithms base   base. log1p(x) computes \\(\\log(1+x)\\) accurately also   \\(|x| \\ll 1\\). exp computes exponential function. expm1(x) computes \\(\\exp(x) - 1\\) accurately also   \\(|x| \\ll 1\\).","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' log(x, base = exp(1))"},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"x numeric complex vector. base positive complex number: base respect     logarithms computed.  Defaults \\(e\\)=exp(1).","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Map dimnames to i,j indices — map_ijx_dimnames","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"Map dimnames ,j indices","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"","code":"map_ijx_dimnames(dbMatrix, colName_i, colName_j)"},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"dbMatrix dbMatrix object colName_i name column rownames add database colName_j name column colnames add database default: 'FALSE'.'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"Constructs table database contains accompanying dimnames dbMatrix. resulting columns table: (row index) colName_i (rownames), j (col index) j_names (colnames) x (counts ,j occcurences)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"Retrieve Set Row (Column) Dimension Names dbMatrix Objects","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' rownames(x)  # S4 method for class 'dbMatrix' rownames(x) <- value  # S4 method for class 'dbMatrix' colnames(x)  # S4 method for class 'dbMatrix' colnames(x) <- value  # S4 method for class 'dbMatrix' dimnames(x)  # S4 method for class 'dbMatrix,list' dimnames(x) <- value"},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"x matrix-like R object, least two dimensions     colnames. value valid value component     dimnames(x).  matrix array either     NULL character vector non-zero length equal     appropriate dimension. .NULL used method. Included compatibility generic. prefix used method. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"Generic function (trimmed) arithmetic mean.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' mean(x, ...)  # S4 method for class 'dbSparseMatrix' mean(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"x dbMatrix object ... arguments passed methods.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":null,"dir":"Reference","previous_headings":"","what":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' nrow(x)  # S4 method for class 'dbMatrix' ncol(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":null,"dir":"Reference","previous_headings":"","what":"Precompute a dbMatrix table in a database — precompute","title":"Precompute a dbMatrix table in a database — precompute","text":"Precomputes dbMatrix table specificied database connection. can speed operations involve breaking sparsity dbSparseMatrix, cases performing + - arithmetic operations. Need run .","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"precompute(conn, m, n, name, verbose = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Precompute a dbMatrix table in a database — precompute","text":"conn duckdb database connection m number rows precomputed dbMatrix table n number columns precomputed dbMatrix table name name precomputed dbMatrix table created verbose logical, print progress messages. default: TRUE.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Precompute a dbMatrix table in a database — precompute","text":"tbl_dbi","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Precompute a dbMatrix table in a database — precompute","text":"num_rows num_cols parameters must exceed maximum row column indices dbMatrix order used densifying dbMatrix. params less maximum row column indices precomputed densification process fail. cases, run function larger n_rows num_cols, manually remove precomputed table set options(dbMatrix.precomp = NULL) R console.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"con = DBI::dbConnect(duckdb::duckdb(), \":memory:\") precompute(con = con , m = 100, n = 100, name = \"precomputed_table\") #> Error in precompute(con = con, m = 100, n = 100, name = \"precomputed_table\"): could not find function \"precompute\""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array(   i = NULL,   j = NULL,   x = NULL,   dims,   rownames = rep(\"\", dims[1]),   fill = \".\",   digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"Calculates mean row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' rowMeans(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' rowMeans(x, ..., memory = FALSE)  # S4 method for class 'dbDenseMatrix' colMeans(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' colMeans(x, ..., memory = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"x NxK matrix-like object, numeric data frame, array-like object two dimensions. ... Additional arguments passed specific methods. memory logical. FALSE (default), results returned dbDenseMatrix. recommended large computations. Set TRUE return results vector. na.rm Always TRUE dbMatrix queries. Included compatibility generic. dims Always 1 dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"Calculates sum row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' rowSums(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' rowSums(x, ..., memory = FALSE)  # S4 method for class 'dbDenseMatrix' colSums(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' colSums(x, ..., memory = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"x NxK matrix-like object, numeric data frame, array-like object two dimensions. ... Additional arguments passed specific methods. memory logical. FALSE (default), results returned dbDenseMatrix. recommended large computations. Set TRUE return results vector. na.rm Always TRUE dbMatrix queries. Included compatibility generic. dims Always 1 dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"Calculates standard deviation row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' colSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbSparseMatrix' colSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbDenseMatrix' rowSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbSparseMatrix' rowSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"x NxK matrix-like object. rows, cols Always NULL dbMatrix queries. Included compatibility generic. na.rm Always TRUE dbMatrix queries. Included compatibility generic. center Always NULL dbMatrix queries. Included compatibility generic. ... Additional arguments passed specific methods. useNames Always TRUE dbMatrix queries. Included compatibility generic. dim Always NULL dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE)  sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50)  sim_denseMat(num_rows = 50, num_cols = 50)  sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42)  sim_dbSparseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"sparse_test\",   memory = FALSE )  sim_dbDenseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"dense_test\",   memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"sum returns sum values   present arguments.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' sum(x, na.rm = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"x dbMatrix object na.rm Always TRUE dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Matrix Transpose — t,dbMatrix-method","title":"Matrix Transpose — t,dbMatrix-method","text":"Given dbMatrix x, t returns transpose x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Matrix Transpose — t,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' t(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Matrix Transpose — t,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Matrix Transpose — t,dbMatrix-method","text":"dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"breaking-changes-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"Rename dbMatrix constructor dbMatrix::dbMatrix().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"Add tests dbMatrix dbDenseMatrix. 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Update .check_overwrite() internal function avoid bug overwritting passed table.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Add initial support reading .mtx files creating dbMatrix objects.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update check_overwrite input validation","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update Royxgen","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Add new precompute function speed matrix densification. Add new show function dbDenseMatrix pretty color better spacing. Add new save function save dbMatrix. Add new input validation functions.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Update docs. Update imports include glue, bit64 crayon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Update constructor calls sim functions. Remove redundant con constructor. Remove db_path constructor. Constructor db_path arg change con object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Add dgTMatrix -memory matrix types supported dbMatrix constructor.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Set :memory: default db_path constructor. Update createDBMatrix docs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Spacing. Update constructor fix. 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Note: operations zero values yet supported dbMatrix objects. addition, certain arithmetic operations dbMatrix objects also yet supported. welcome user feedback reporting issues Github page.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) #> Loading required package: Matrix #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #>   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #>   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #>   ..@ Dim     : int [1:2] 634 624 #>   ..@ Dimnames:List of 2 #>   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #>   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #>   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #>   ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\")  dbsm <- dbMatrix(value = dgc,                   con = con,                   name = 'visium',                   class = \"dbSparseMatrix\",                  overwrite = TRUE)  # preview the object dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> ℹ Densifying 'dbSparseMatrix' on the fly... #> 634 x 624  matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                    #> Gna12         2 3 2 2 10 2 4 6 4 1 #> Ccnd2         1 2 2 1  1 2 1 2 2 1 #> Btbd17        1 2 2 2  1 1 3 1 1 1 #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       1 2 1 1  1 1 1 1 1 1 #> 9630013A20Rik 1 1 1 1  1 1 1 1 1 1 #> 2900040C04Rik 2 1 1 1  1 1 1 1 1 2  dbsm * 100 #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                                       #> Gna12         100 200 100 100 900 100 300 500 300   . #> Ccnd2           . 100 100   .   . 100   . 100 100   . #> Btbd17          . 100 100 100   .   . 200   .   .   . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935         . 100   .   .   .   .   .   .   .   . #> 9630013A20Rik   .   .   .   .   .   .   .   .   .   . #> 2900040C04Rik 100   .   .   .   .   .   .   .   . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         2 4 2 2 18 2 6 10 6 . #> Ccnd2         . 2 2 .  . 2 .  2 2 . #> Btbd17        . 2 2 2  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 2 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 2 . . .  . . .  . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"dbMatrix arithmetic > Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         1 4 1 1 81 1 9 25 9 . #> Ccnd2         . 1 1 .  . 1 .  1 1 . #> Btbd17        . 1 1 1  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 1 . . .  . . .  . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"dbMatrix arithmetic > Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"dbMatrix arithmetic","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] Matrix_1.7-0        dbMatrix_0.0.0.9023 #>  #> loaded via a namespace (and not attached): #>  [1] bit_4.0.5             jsonlite_1.8.8        crayon_1.5.3          #>  [4] dplyr_1.1.4           compiler_4.4.1        tidyselect_1.2.1      #>  [7] blob_1.2.4            jquerylib_0.1.4       systemfonts_1.1.0     #> [10] textshaping_0.4.0     yaml_2.3.10           fastmap_1.2.0         #> [13] lattice_0.22-6        R6_2.5.1              generics_0.1.3        #> [16] knitr_1.48            tibble_3.2.1          desc_1.4.3            #> [19] MatrixGenerics_1.16.0 DBI_1.2.3             bslib_0.8.0           #> [22] pillar_1.9.0          rlang_1.1.4           utf8_1.2.4            #> [25] cachem_1.1.0          xfun_0.47             fs_1.6.4              #> [28] sass_0.4.9            bit64_4.0.5           cli_3.6.3             #> [31] withr_3.0.1           pkgdown_2.1.1         magrittr_2.0.3        #> [34] digest_0.6.37         grid_4.4.1            dbplyr_2.5.0          #> [37] lifecycle_1.0.4       vctrs_0.6.5           evaluate_1.0.0        #> [40] glue_1.7.0            data.table_1.16.0     duckdb_1.0.0-2        #> [43] ragg_1.3.3            fansi_1.0.6           purrr_1.0.2           #> [46] rmarkdown_2.28        matrixStats_1.4.1     tools_4.4.1           #> [49] pkgconfig_2.0.3       htmltools_0.5.8.1"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix objects currently support several statistical matrix operations listed support coming soon. ✅ - implemented 🟧 - yet implemented","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ##   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ##   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ##   ..@ Dim     : int [1:2] 634 624 ##   ..@ Dimnames:List of 2 ##   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ##   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ##   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ##   ..@ factors : list() # create dbSparseMatrix from the same dgc con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\")  sparse <- dbMatrix(value = dgc,                     con = con,                     name = 'visium',                     class = \"dbSparseMatrix\",                    overwrite = TRUE)  # preview  # show function aims to emulate the show method for dgCMatrix head(sparse) ## 6 x 624  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                   ## Gna12         1 2 1 1 9 1 3 5 3 . ##  [ reached getOption(\"max.print\") -- omitted 633 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## 624 x 634  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ##                                        ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ##  ## ......suppressing 624 columns and 618 rows ##  ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## 1 x 624  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                                                             ## row1 0.74132 1.32965 1.14353 0.83438 1.61356 2.21293 1.7224 1.90221 0.73975 ##              ## row1 0.92587"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## 1 x 624  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                                                  ## row1 470 843 725 529 1023 1403 1092 1206 469 587"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ## 634 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                       ## Gna12         2.71795 ## Ccnd2         1.73237 ## Btbd17        0.55288 ##  ## ......suppressing 628 rows ##  ## Gm19935       0.20833 ## 9630013A20Rik 0.17147 ## 2900040C04Rik 0.15545"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ## 634 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                    ## Gna12         1696 ## Ccnd2         1081 ## Btbd17         345 ##  ## ......suppressing 628 rows ##  ## Gm19935        130 ## 9630013A20Rik  107 ## 2900040C04Rik   97"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 624\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 624\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 634\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\" all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] \"Modes: S4, numeric\"                                                  ## [2] \"Lengths: 1, 634\"                                                     ## [3] \"names for current but not for target\"                                ## [4] \"Attributes: < names for target but not for current >\"                ## [5] \"Attributes: < Length mismatch: comparison on first 0 components >\""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix()  # preview dense ## 50 x 50  matrix of class \"dbDenseMatrix\" ##                                                                               ## row1   1.37096  0.32193  1.20097  -0.0407 -2.00093 -1.09616 -0.00462  0.72417 ##                         ## row1   1.33491 -1.30382 ##  ## ......suppressing 40 columns and 44 rows ##  ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## 50 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ##                                                                               ## col1   1.37096  -0.5647  0.36313  0.63286  0.40427 -0.10612  1.51152 -0.09466 ##                         ## col1   2.01842 -0.06271 ##  ## ......suppressing 40 columns and 44 rows ##  ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ## 1 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'col1', 'col2', 'col3' ... suppressing 44 ...'col48', 'col49', 'col50' ]] ##                                                                           ## row1 -0.03562 0.10074 -0.15122 -0.02372 0.00794 -0.02862 -0.06156 0.12742 ##                        ## row1 -0.11944 -0.11622"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ## 1 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'col1', 'col2', 'col3' ... suppressing 44 ...'col48', 'col49', 'col50' ]] ## Warning: ORDER BY is ignored in subqueries without LIMIT ## ℹ Do you need to move arrange() later in the pipeline or use window_order() instead? ##                                                                         ## row1 -1.781 5.037 -7.561 -1.186 0.397 -1.431 -3.078 6.371 -5.972 -5.811"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ## 50 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ##                ## row1   0.05362 ## row2   0.00246 ## row3   0.03132 ##  ## ......suppressing 44 rows ##  ## row48 -0.10104 ## row49  0.05928 ## row50  0.02156"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ## 50 x 1  matrix of class \"dbDenseMatrix\" ## [[ Colnames: 'col1' ]] ## Warning: ORDER BY is ignored in subqueries without LIMIT ## ℹ Do you need to move arrange() later in the pipeline or use window_order() instead? ##              ## row1   2.681 ## row2   0.123 ## row3   1.566 ##  ## ......suppressing 44 rows ##  ## row48 -5.052 ## row49  2.964 ## row50  1.078"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.0096724"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8    LC_NUMERIC=C        LC_TIME=C.UTF-8     ##  [4] LC_COLLATE=C.UTF-8  LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ##  [7] LC_PAPER=C.UTF-8    LC_NAME=C           LC_ADDRESS=C        ## [10] LC_TELEPHONE=C      ##  [ reached getOption(\"max.print\") -- omitted 2 entries ] ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] Matrix_1.7-0        dbMatrix_0.0.0.9023 ##  ## loaded via a namespace (and not attached): ##  [1] jsonlite_1.8.8    crayon_1.5.3      dplyr_1.1.4       compiler_4.4.1    ##  [5] tidyselect_1.2.1  blob_1.2.4        jquerylib_0.1.4   systemfonts_1.1.0 ##  [9] textshaping_0.4.0 yaml_2.3.10       ##  [ reached getOption(\"max.print\") -- omitted 38 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author, maintainer. Jiaji George Chen. Author. Ruben Dries. Author.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9023, https://drieslab.github.io/dbMatrix/.","code":"@Manual{,   title = {dbMatrix: dbMatrix},   author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries},   year = {2024},   note = {R package version 0.0.0.9023},   url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations. Note: Work progress! Bugs unexpected behavior likely occur. welcome user feedback reporting issues Github page.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"Converts dbMatrix object -memory matrix sparse matrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' as.matrix(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"x dbMatrix object (dbSparseMatrix dbDenseMatrix) ... Additional arguments (used)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"Matrix::dgCMatrix base R matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/as.matrix-dbMatrix-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert dbMatrix to in-memory matrix — as.matrix,dbMatrix-method","text":"method converts dbMatrix object (dbSparseMatrix dbDenseMatrix) -memory Matrix::dgCMatrix (sparse) base R matrix (dense). Warning: can cause memory issues input matrix large.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":null,"dir":"Reference","previous_headings":"","what":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"Pretty prints tables, temporary tables, views database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"","code":"# S4 method for class 'DBIConnection' dbList(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"conn DBIConnection object, returned dbConnect().","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbList-DBIConnection-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List remote tables, temporary tables, and views — dbList,DBIConnection-method","text":"Similar DBI::dbListTables, categorizes tables three categories: Tables Temporary Tables (removed connection closed) Views (may removed connection closed)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"","code":"dbMatrix(   value,   class = NULL,   con = NULL,   overwrite = FALSE,   name = \"dbMatrix\",   dims = NULL,   dim_names = NULL,   mtx_rowname_file_path,   mtx_rowname_col_idx = 1,   mtx_colname_file_path,   mtx_colname_col_idx = 1,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) con DBI duckdb connection object (required) overwrite whether overwrite table already exists database (required) name table name assign within database (required, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) mtx_rowname_file_path path .mtx rowname file read (optional) database. default, header assumed. mtx_rowname_col_idx column index row name file (optional) mtx_colname_file_path path .mtx colname file read database. default, header assumed. (optional) mtx_colname_col_idx column index column name file (optional) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"function reads data pre-existing DuckDB database. Supported value data types: dgCMatrix -memory sparse matrix Matrix package dgTMatrix -memory triplet vector COO matrix matrix -memory dense matrix base R .mtx Path .mtx file .csv Path .csv file tbl_duckdb_connection Table DuckDB database ijx format existing dbMatrix object. dims dim_names must specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a dbSparseMatrix or dbDenseMatrix object — dbMatrix","text":"","code":"dgc = readRDS(system.file(\"data\", \"dgc.rds\", package = \"dbMatrix\")) #> Loading required package: Matrix con <- DBI::dbConnect(duckdb::duckdb(), \":memory:\") dbSparse <- dbMatrix(   value = dgc,   con = con,   name = \"sparse_matrix\",   class = \"dbSparseMatrix\",   overwrite = TRUE ) dbSparse #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":null,"dir":"Reference","previous_headings":"","what":"dbMatrix_from_tbl — dbMatrix_from_tbl","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"Construcst dbSparseMatrix object tbl_duckdb_connection object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"","code":"dbMatrix_from_tbl(   tbl,   rownames_colName,   colnames_colName,   name = \"dbMatrix\",   overwrite = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"tbl tbl_duckdb_connection table DuckDB database long format rownames_colName character column name rownames tbl (required) colnames_colName character column name colnames tbl (required) name table name assign within database (required, default: \"dbMatrix\") overwrite whether overwrite table already exists database (required) con DBI duckdb connection object (required)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix_from_tbl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"dbMatrix_from_tbl — dbMatrix_from_tbl","text":"tbl_duckdb_connection object must contain dimension names.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimensions of an Object — dim,dbMatrix-method","title":"Dimensions of an Object — dim,dbMatrix-method","text":"Retrieve dimension object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimensions of an Object — dim,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dim-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimensions of an Object — dim,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for conn arg — .check_con","title":"Input validation for conn arg — .check_con","text":"Input validation conn arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for conn arg — .check_con","text":"","code":".check_con(conn)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for conn arg — .check_con","text":"conn tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for name arg — .check_name","title":"Input validation for name arg — .check_name","text":"Input validation name arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for name arg — .check_name","text":"","code":".check_name(name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for overwrite arg — .check_overwrite","title":"Input validation for overwrite arg — .check_overwrite","text":"Input validation overwrite arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_overwrite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for overwrite arg — .check_overwrite","text":"","code":".check_overwrite(conn, overwrite, name, skip_value_check = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":null,"dir":"Reference","previous_headings":"","what":"Input validation for data arg — .check_value","title":"Input validation for data arg — .check_value","text":"Input validation data arg","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Input validation for data arg — .check_value","text":"","code":".check_value(value)"},{"path":"https://drieslab.github.io/dbMatrix/reference/dot-check_value.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Input validation for data arg — .check_value","text":"x Matrix, matrix, tbl_duckdb_connection object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dim — get_MM_dim","title":"get_MM_dim — get_MM_dim","text":"Internal function read dimensions .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dim — get_MM_dim","text":"","code":"get_MM_dim(mtx_file_path)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dim — get_MM_dim","text":"mtx_file_path path .mtx file read database","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dim — get_MM_dim","text":"integer vector dimensions","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dim.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dim — get_MM_dim","text":"Scans header mtx file (starting %) takes one line representing dimensions number nonzero values. Note: header size can vary depending .mtx file.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"get_MM_dimnames — get_MM_dimnames","title":"get_MM_dimnames — get_MM_dimnames","text":"Internal function read row column names .mtx file","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_MM_dimnames — get_MM_dimnames","text":"","code":"get_MM_dimnames(   mtx_file_path,   mtx_rowname_file_path,   mtx_rowname_col_idx = 1,   mtx_colname_file_path,   mtx_colname_col_idx = 1,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_MM_dimnames — get_MM_dimnames","text":"mtx_file_path path .mtx file read database mtx_rowname_file_path path .mtx rowname file read database. default, header assumed. mtx_rowname_col_idx column index row name file mtx_colname_file_path path .mtx colname file read database. default, header assumed. mtx_colname_col_idx column index column name file ... additional params pass data.table::fread","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_MM_dimnames — get_MM_dimnames","text":"list row column name character vectors","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_MM_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"get_MM_dimnames — get_MM_dimnames","text":"Can used read row column names .mtx files. Note: files must contain header (colnames). mtx_rowname_col_idx mtx_colname_col_idx can used specify column index row column name files, respectively. default, first column used . TODO: Support reading rownames colnames.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the First or Last Parts of an Object — head,dbMatrix-method","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"Returns first last parts vector, matrix, table, data frame   function.  Since head() tail() generic   functions, may also extended classes.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' head(x, n = 6L, ...)  # S4 method for class 'dbMatrix' tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head_tail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the First or Last Parts of an Object — head,dbMatrix-method","text":"x object n integer vector length dim(x) (1,     non-dimensioned objects).  logical silently coerced     integer.  Values specify indices     selected corresponding dimension (along length)     object. positive value n[] includes first/last     n[] indices dimension, negative value     excludes last/first abs(n[]), including remaining     indices. NA non-specified values (length(n) <       length(dim(x))) select indices dimension. Must     contain least one non-missing value. ... arguments passed methods.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Logarithms and Exponentials — log,dbMatrix-method","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"log computes logarithms, default natural logarithms,   log10 computes common (.e., base 10) logarithms,   log2 computes binary (.e., base 2) logarithms.   general form log(x, base) computes logarithms base   base. log1p(x) computes \\(\\log(1+x)\\) accurately also   \\(|x| \\ll 1\\). exp computes exponential function. expm1(x) computes \\(\\exp(x) - 1\\) accurately also   \\(|x| \\ll 1\\).","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' log(x, base = exp(1))"},{"path":"https://drieslab.github.io/dbMatrix/reference/log-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logarithms and Exponentials — log,dbMatrix-method","text":"x numeric complex vector. base positive complex number: base respect     logarithms computed.  Defaults \\(e\\)=exp(1).","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Map dimnames to i,j indices — map_ijx_dimnames","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"Map dimnames ,j indices","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"","code":"map_ijx_dimnames(dbMatrix, colName_i, colName_j)"},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"dbMatrix dbMatrix object colName_i name column rownames add database colName_j name column colnames add database default: 'FALSE'.'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/map_ijx_dimnames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Map dimnames to i,j indices — map_ijx_dimnames","text":"Constructs table database contains accompanying dimnames dbMatrix. resulting columns table: (row index) colName_i (rownames), j (col index) j_names (colnames) x (counts ,j occcurences)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"Retrieve Set Row (Column) Dimension Names dbMatrix Objects","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' rownames(x)  # S4 method for class 'dbMatrix' rownames(x) <- value  # S4 method for class 'dbMatrix' colnames(x)  # S4 method for class 'dbMatrix' colnames(x) <- value  # S4 method for class 'dbMatrix' dimnames(x)  # S4 method for class 'dbMatrix,list' dimnames(x) <- value"},{"path":"https://drieslab.github.io/dbMatrix/reference/matrix_props.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve and Set Row (Column) Dimension Names of dbMatrix Objects — rownames,dbMatrix-method","text":"x matrix-like R object, least two dimensions     colnames. value valid value component     dimnames(x).  matrix array either     NULL character vector non-zero length equal     appropriate dimension. .NULL used method. Included compatibility generic. prefix used method. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"Generic function (trimmed) arithmetic mean.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' mean(x, ...)  # S4 method for class 'dbSparseMatrix' mean(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arithmetic Mean for dbMatrix objects — mean,dbDenseMatrix-method","text":"x dbMatrix object ... arguments passed methods.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":null,"dir":"Reference","previous_headings":"","what":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' nrow(x)  # S4 method for class 'dbMatrix' ncol(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow_ncol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The Number of Rows/Columns of a dbMatrix Object — nrow,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":null,"dir":"Reference","previous_headings":"","what":"Precompute a dbMatrix table in a database — precompute","title":"Precompute a dbMatrix table in a database — precompute","text":"Precomputes dbMatrix table specificied database connection. can speed operations involve breaking sparsity dbSparseMatrix, cases performing + - arithmetic operations. Need run .","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"precompute(conn, m, n, name, verbose = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Precompute a dbMatrix table in a database — precompute","text":"conn duckdb database connection m number rows precomputed dbMatrix table n number columns precomputed dbMatrix table name name precomputed dbMatrix table created verbose logical, print progress messages. default: TRUE.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Precompute a dbMatrix table in a database — precompute","text":"tbl_dbi","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Precompute a dbMatrix table in a database — precompute","text":"num_rows num_cols parameters must exceed maximum row column indices dbMatrix order used densifying dbMatrix. params less maximum row column indices precomputed densification process fail. cases, run function larger n_rows num_cols, manually remove precomputed table set options(dbMatrix.precomp = NULL) R console.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/precompute.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Precompute a dbMatrix table in a database — precompute","text":"","code":"con = DBI::dbConnect(duckdb::duckdb(), \":memory:\") precompute(con = con , m = 100, n = 100, name = \"precomputed_table\") #> Error in precompute(con = con, m = 100, n = 100, name = \"precomputed_table\"): could not find function \"precompute\""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array(   i = NULL,   j = NULL,   x = NULL,   dims,   rownames = rep(\"\", dims[1]),   fill = \".\",   digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"Calculates mean row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' rowMeans(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' rowMeans(x, ..., memory = FALSE)  # S4 method for class 'dbDenseMatrix' colMeans(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' colMeans(x, ..., memory = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_means.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) means for dbMatrix objects — rowMeans,dbDenseMatrix-method","text":"x NxK matrix-like object, numeric data frame, array-like object two dimensions. ... Additional arguments passed specific methods. memory logical. FALSE (default), results returned dbDenseMatrix. recommended large computations. Set TRUE return results vector. na.rm Always TRUE dbMatrix queries. Included compatibility generic. dims Always 1 dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"Calculates sum row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' rowSums(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' rowSums(x, ..., memory = FALSE)  # S4 method for class 'dbDenseMatrix' colSums(x, ..., memory = FALSE)  # S4 method for class 'dbSparseMatrix' colSums(x, ..., memory = FALSE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/row_col_sums.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) sums for dbMatrix objects — rowSums,dbDenseMatrix-method","text":"x NxK matrix-like object, numeric data frame, array-like object two dimensions. ... Additional arguments passed specific methods. memory logical. FALSE (default), results returned dbDenseMatrix. recommended large computations. Set TRUE return results vector. na.rm Always TRUE dbMatrix queries. Included compatibility generic. dims Always 1 dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":null,"dir":"Reference","previous_headings":"","what":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"Calculates standard deviation row (column) matrix-like object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"","code":"# S4 method for class 'dbDenseMatrix' colSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbSparseMatrix' colSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbDenseMatrix' rowSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )  # S4 method for class 'dbSparseMatrix' rowSds(   x,   rows = NULL,   cols = NULL,   na.rm = FALSE,   center = NULL,   ...,   useNames = TRUE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/sds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row (column) standard deviations for dbMatrix objects — colSds,dbDenseMatrix-method","text":"x NxK matrix-like object. rows, cols Always NULL dbMatrix queries. Included compatibility generic. na.rm Always TRUE dbMatrix queries. Included compatibility generic. center Always NULL dbMatrix queries. Included compatibility generic. ... Additional arguments passed specific methods. useNames Always TRUE dbMatrix queries. Included compatibility generic. dim Always NULL dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE)  sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50)  sim_denseMat(num_rows = 50, num_cols = 50)  sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42)  sim_dbSparseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"sparse_test\",   memory = FALSE )  sim_dbDenseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"dense_test\",   memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"sum returns sum values   present arguments.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' sum(x, na.rm = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/reference/sum-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sum of Vector Elements in dbMatrix objects — sum,dbMatrix-method","text":"x dbMatrix object na.rm Always TRUE dbMatrix queries. Included compatibility generic.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Matrix Transpose — t,dbMatrix-method","title":"Matrix Transpose — t,dbMatrix-method","text":"Given dbMatrix x, t returns transpose x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Matrix Transpose — t,dbMatrix-method","text":"","code":"# S4 method for class 'dbMatrix' t(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Matrix Transpose — t,dbMatrix-method","text":"x dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/t-dbMatrix-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Matrix Transpose — t,dbMatrix-method","text":"dbMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"breaking-changes-0-0-0-9023","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"dbMatrix 0.0.0.9023 (2024-09-18)","text":"dbMatrix summary methods now return dbDenseMatrix objects instead -memory vectors. Removed colTypes castNumeric. Removed @name check initialize.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9023","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9023 (2024-09-18)","text":"New compute method saving dbMatrix objects. writes dbMatrix object table database along row column names (e.g. ‘dbMatrixname_rownames’). New load method loading computed dbMatrix objects. dbMatrix::compute() method must called loading object. Updated .check_overwrite allow passing overwrite arg. New internal function write_dimnames enable saving dbMatrix objects. New sum method dbMatrix objects. Improvements precomputed table: Use existing precomputed table db available. Improvements precomputed table: Transpose precomputed table sufficient dimensions exists instead creating new one. done via TEMPORARY VIEW avoid writing disk modifying existing precomputed table may referenced tables. Custom SQL statement todbDense conversion creates TEMPORARY VIEW name dbDenseMatrix_hash.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9023","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9023 (2024-09-18)","text":"Update whitespace. Update dbMatrix constructor roxygen. Update roxygen toDbDense.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"docs-0-0-0-9023","dir":"Changelog","previous_headings":"","what":"Docs","title":"dbMatrix 0.0.0.9023 (2024-09-18)","text":"Update reference page. Update mean documentation. Update log documentation. Update roxygen.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9023","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9023 (2024-09-18)","text":"recycle matrix needed.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"breaking-changes-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"Rename dbMatrix constructor dbMatrix::dbMatrix().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"Add tests dbMatrix dbDenseMatrix. Add internal function map_ijx_dimnames. Add internal function dbMatrix_from_tbl. Extract now constructs unique temporary virtual tables arrow schema.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"Document pkgdown website. Add cli imports. Update generics.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9022","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9022 (2024-08-14)","text":"explicit non-supported Arith Ops operations. Fix show() method dbDenseMatrix objects.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9021","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9021 (2024-07-05)","text":"Improve show function dbDenseMatrix. Updated simulate functions include overwrite param. Update .check_overwrite() internal function avoid bug overwritting passed table.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Add initial support reading .mtx files creating dbMatrix objects.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update check_overwrite input validation","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9020","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9020 (2024-07-05)","text":"Update Royxgen","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Add new precompute function speed matrix densification. Add new show function dbDenseMatrix pretty color better spacing. Add new save function save dbMatrix. Add new input validation functions.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9019","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9019 (2024-03-18)","text":"Update docs. Update imports include glue, bit64 crayon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Update constructor calls sim functions. Remove redundant con constructor. Remove db_path constructor. Constructor db_path arg change con object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Add dgTMatrix -memory matrix types supported dbMatrix constructor.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Set :memory: default db_path constructor. Update createDBMatrix docs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9018","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9018 (2024-02-12)","text":"Spacing. Update constructor fix. Remove :temp: place :memory:.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove “:temp:” tests. Replace ‘:temp:’ ‘:memory:’. Add matrix addition dgCMatrix as_ijx().","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Add unit tests scalar arith. Add unit tests names.R.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9017","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9017 (2024-02-07)","text":"Remove random browser() call. Add MatrixGenerics deps. Update gitignore.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9016","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9016 (2024-01-23)","text":"Add boolean indexing tests test-extract.R. Add as_ijx() convenience function. Update createDBMatrix() use dplyr::copy_to(). Update as_matrix() convenience function. Add unit tests extract methods.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Add log(). Update toDbDense use dplyr instead SQL.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9015","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9015 (2024-01-22)","text":"Update DESCRIPTION include testthat. Update docs.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9014","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9014 (2024-01-19)","text":"update dbIndex superclass update as_matrix()","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Rename update dbIndex superclass fix indexing bugs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Add experimental as_matrix() convenience function.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update docs. 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