From cfdc4f3a618e460b4a8c9333a9724e824f18bee4 Mon Sep 17 00:00:00 2001
From: Gao Wang <wangow@gmail.com>
Date: Thu, 26 Oct 2023 14:01:22 -0400
Subject: [PATCH] Update documentation

---
 _sources/code/fine_mapping/SuSiE/SuSiE.ipynb | 9 ++++-----
 code/fine_mapping/SuSiE/SuSiE.html           | 9 ++++-----
 searchindex.js                               | 2 +-
 3 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/_sources/code/fine_mapping/SuSiE/SuSiE.ipynb b/_sources/code/fine_mapping/SuSiE/SuSiE.ipynb
index b892aab57..fe8a8ef97 100644
--- a/_sources/code/fine_mapping/SuSiE/SuSiE.ipynb
+++ b/_sources/code/fine_mapping/SuSiE/SuSiE.ipynb
@@ -385,7 +385,6 @@
     "                             refine=TRUE,\n",
     "                             compute_univariate_zscore=FALSE,\n",
     "                             coverage=${coverage})\n",
-    "            fitted[[r]]$sets_secondary = susie_get_cs(fitted[[r]], fdat$residual_X_scaled[[r]], coverage=${secondary_coverage})\n",
     "            fitted[[r]]$analysis_time <- proc.time() - st\n",
     "            fitted[[r]] <- post_process_susie(fitted[[r]], fdat, r, signal_cutoff = ${pip_cutoff})\n",
     "            if (!is.null(fitted[[r]]$sets$cs)) {\n",
@@ -400,13 +399,13 @@
     "        }\n",
     "      # generate weights for TWAS using some alternative approaches --- this is not exactly fine-mapping but makes sense to do it here for data production\n",
     "      fitted[[r]]$susie_weights = susie_weights(fdat$fitted[[r]])\n",
-    "      fitted[[r]]$susie_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$susie_weights, fdat$residual_Y_scaled[[r]])\n",
+    "      fitted[[r]]$susie_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$susie_weights, fdat$residual_Y_scaled[[r]])^2\n",
     "      fitted[[r]]$enet_weights = glmnet_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]])\n",
-    "      fitted[[r]]$enet_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$enet_weights, fdat$residual_Y_scaled[[r]])\n",
+    "      fitted[[r]]$enet_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$enet_weights, fdat$residual_Y_scaled[[r]])^2\n",
     "      fitted[[r]]$lasso_weights = glmnet_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]], alpha = 1)\n",
-    "      fitted[[r]]$lasso_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$lasso_weights, fdat$residual_Y_scaled[[r]])\n",
+    "      fitted[[r]]$lasso_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$lasso_weights, fdat$residual_Y_scaled[[r]])^2\n",
     "      fitted[[r]]$mr_ash_weights = mr_ash_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]], beta.init=fitted[[r]]$lasso_weights)\n",
-    "      fitted[[r]]$mr_ash_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$mr_ash_weights, fdat$residual_Y_scaled[[r]])\n",
+    "      fitted[[r]]$mr_ash_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$mr_ash_weights, fdat$residual_Y_scaled[[r]])^2\n",
     "    }\n",
     "    names(fitted) <- names(fdat$residual_Y_scaled)\n",
     "    saveRDS(fitted, ${_output:ar}, compress='xz')"
diff --git a/code/fine_mapping/SuSiE/SuSiE.html b/code/fine_mapping/SuSiE/SuSiE.html
index 9bdb16afa..fd1a169c0 100644
--- a/code/fine_mapping/SuSiE/SuSiE.html
+++ b/code/fine_mapping/SuSiE/SuSiE.html
@@ -782,7 +782,6 @@ <h2>Univariate SuSiE<a class="headerlink" href="#univariate-susie" title="Permal
                              refine=TRUE,
                              compute_univariate_zscore=FALSE,
                              coverage=${coverage})
-            fitted[[r]]$sets_secondary = susie_get_cs(fitted[[r]], fdat$residual_X_scaled[[r]], coverage=${secondary_coverage})
             fitted[[r]]$analysis_time &lt;- proc.time() - st
             fitted[[r]] &lt;- post_process_susie(fitted[[r]], fdat, r, signal_cutoff = ${pip_cutoff})
             if (!is.null(fitted[[r]]$sets$cs)) {
@@ -797,13 +796,13 @@ <h2>Univariate SuSiE<a class="headerlink" href="#univariate-susie" title="Permal
         }
       # generate weights for TWAS using some alternative approaches --- this is not exactly fine-mapping but makes sense to do it here for data production
       fitted[[r]]$susie_weights = susie_weights(fdat$fitted[[r]])
-      fitted[[r]]$susie_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$susie_weights, fdat$residual_Y_scaled[[r]])
+      fitted[[r]]$susie_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$susie_weights, fdat$residual_Y_scaled[[r]])^2
       fitted[[r]]$enet_weights = glmnet_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]])
-      fitted[[r]]$enet_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$enet_weights, fdat$residual_Y_scaled[[r]])
+      fitted[[r]]$enet_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$enet_weights, fdat$residual_Y_scaled[[r]])^2
       fitted[[r]]$lasso_weights = glmnet_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]], alpha = 1)
-      fitted[[r]]$lasso_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$lasso_weights, fdat$residual_Y_scaled[[r]])
+      fitted[[r]]$lasso_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$lasso_weights, fdat$residual_Y_scaled[[r]])^2
       fitted[[r]]$mr_ash_weights = mr_ash_weights(fdat$residual_X_scaled[[r]], fdat$residual_Y_scaled[[r]], beta.init=fitted[[r]]$lasso_weights)
-      fitted[[r]]$mr_ash_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$mr_ash_weights, fdat$residual_Y_scaled[[r]])
+      fitted[[r]]$mr_ash_r2 = cor(fdat$residual_X_scaled[[r]] %*% fitted[[r]]$mr_ash_weights, fdat$residual_Y_scaled[[r]])^2
     }
     names(fitted) &lt;- names(fdat$residual_Y_scaled)
     saveRDS(fitted, ${_output:ar}, compress=&#39;xz&#39;)
diff --git a/searchindex.js b/searchindex.js
index 6d642aa65..1b1ea5b35 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["README", "code/association_scan/APEX/APEX", "code/association_scan/TensorQTL/TensorQTL", "code/association_scan/qtl_association_postprocessing", "code/association_scan/qtl_association_testing", "code/commands_generator/bulk_expression_commands", "code/commands_generator/eQTL_analysis_commands", "code/data_preprocessing/covariate/covariate_formatting", "code/data_preprocessing/covariate/covariate_hidden_factor", "code/data_preprocessing/covariate_preprocessing", "code/data_preprocessing/genotype/GRM", "code/data_preprocessing/genotype/GWAS_QC", "code/data_preprocessing/genotype/PCA", "code/data_preprocessing/genotype/VCF_QC", "code/data_preprocessing/genotype/genotype_formatting", "code/data_preprocessing/genotype_preprocessing", "code/data_preprocessing/phenotype/gene_annotation", "code/data_preprocessing/phenotype/phenotype_formatting", "code/data_preprocessing/phenotype/phenotype_imputation", "code/data_preprocessing/phenotype_preprocessing", "code/data_preprocessing/reference_data", "code/fine_mapping/SuSiE/SuSiE", "code/fine_mapping/SuSiE/SuSiE_RSS", "code/fine_mapping/multivariate_fine_mapping", "code/fine_mapping/univariate_fine_mapping", "code/integrative_analysis/COLOC/fastenloc_dap", "code/integrative_analysis/COLOC/mvenloc", "code/integrative_analysis/colocalization", "code/integrative_analysis/enrichment/gwas_enrichment", "code/integrative_analysis/enrichment/ldsc", "code/integrative_analysis/functional_annotation", "code/misc/rds_to_vcf", "code/misc/summary_stats_standardizer", "code/molecular_phenotypes/QC/bulk_expression_QC", "code/molecular_phenotypes/QC/bulk_expression_normalization", "code/molecular_phenotypes/QC/splicing_normalization", "code/molecular_phenotypes/apa", "code/molecular_phenotypes/bulk_expression", "code/molecular_phenotypes/calling/RNA_calling", "code/molecular_phenotypes/calling/apa_calling", "code/molecular_phenotypes/calling/methylation_calling", "code/molecular_phenotypes/calling/splicing_calling", "code/molecular_phenotypes/methylation", "code/molecular_phenotypes/scnuc_expression", "code/molecular_phenotypes/splicing", "code/multivariate/MASH/fastqtl_to_mash", "code/multivariate/MASH/mixture_prior", "code/multivariate/MASH_pipeline", "code/multivariate/METAL/METAL", "code/multivariate/METAL_pipeline", "code/xqtl_protocol_demo"], "filenames": ["README.md", "code/association_scan/APEX/APEX.ipynb", "code/association_scan/TensorQTL/TensorQTL.ipynb", "code/association_scan/qtl_association_postprocessing.ipynb", "code/association_scan/qtl_association_testing.ipynb", "code/commands_generator/bulk_expression_commands.ipynb", "code/commands_generator/eQTL_analysis_commands.ipynb", "code/data_preprocessing/covariate/covariate_formatting.ipynb", "code/data_preprocessing/covariate/covariate_hidden_factor.ipynb", "code/data_preprocessing/covariate_preprocessing.ipynb", "code/data_preprocessing/genotype/GRM.ipynb", "code/data_preprocessing/genotype/GWAS_QC.ipynb", "code/data_preprocessing/genotype/PCA.ipynb", "code/data_preprocessing/genotype/VCF_QC.ipynb", "code/data_preprocessing/genotype/genotype_formatting.ipynb", "code/data_preprocessing/genotype_preprocessing.ipynb", "code/data_preprocessing/phenotype/gene_annotation.ipynb", "code/data_preprocessing/phenotype/phenotype_formatting.ipynb", "code/data_preprocessing/phenotype/phenotype_imputation.ipynb", "code/data_preprocessing/phenotype_preprocessing.ipynb", "code/data_preprocessing/reference_data.ipynb", "code/fine_mapping/SuSiE/SuSiE.ipynb", "code/fine_mapping/SuSiE/SuSiE_RSS.ipynb", "code/fine_mapping/multivariate_fine_mapping.ipynb", "code/fine_mapping/univariate_fine_mapping.ipynb", "code/integrative_analysis/COLOC/fastenloc_dap.ipynb", "code/integrative_analysis/COLOC/mvenloc.ipynb", "code/integrative_analysis/colocalization.ipynb", "code/integrative_analysis/enrichment/gwas_enrichment.ipynb", "code/integrative_analysis/enrichment/ldsc.ipynb", "code/integrative_analysis/functional_annotation.ipynb", "code/misc/rds_to_vcf.ipynb", "code/misc/summary_stats_standardizer.ipynb", "code/molecular_phenotypes/QC/bulk_expression_QC.ipynb", "code/molecular_phenotypes/QC/bulk_expression_normalization.ipynb", "code/molecular_phenotypes/QC/splicing_normalization.ipynb", "code/molecular_phenotypes/apa.ipynb", "code/molecular_phenotypes/bulk_expression.ipynb", "code/molecular_phenotypes/calling/RNA_calling.ipynb", "code/molecular_phenotypes/calling/apa_calling.ipynb", "code/molecular_phenotypes/calling/methylation_calling.ipynb", "code/molecular_phenotypes/calling/splicing_calling.ipynb", "code/molecular_phenotypes/methylation.ipynb", "code/molecular_phenotypes/scnuc_expression.ipynb", "code/molecular_phenotypes/splicing.ipynb", "code/multivariate/MASH/fastqtl_to_mash.ipynb", "code/multivariate/MASH/mixture_prior.ipynb", "code/multivariate/MASH_pipeline.ipynb", "code/multivariate/METAL/METAL.ipynb", "code/multivariate/METAL_pipeline.ipynb", "code/xqtl_protocol_demo.ipynb"], "titles": ["FunGen-xQTL Computational Protocol", "APEX QTL association testing", "TensorQTL QTL association testing", "QTL data postprocessing", "QTL association analysis", "RNA-seq calling and QC", "Univariate xQTL Discovery", "Covariate data formatting", "Hidden factor analysis", "Covariate data preprocessing", "Genomic relationship matrices", "Genotype PLINK file quality control", "Principal component analysis", "Genotype VCF file quality control", "Genotype data formatting", "Genotype data preprocessing", "Gene coordinate annotation", "Phenotype data formatting", "Phenotype data imputation", "Phenotype data preprocessing", "Reference data standardization", "Fine-mapping with individual level data", "Fine-mapping with SuSiE RSS model", "Multivariate fine-mapping workflows", "Univariate fine-mapping workflows", "Colocalization with FastENLOC", "Multivariate SuSiE and ENLOC model", "QTL and GWAS Colocalization", "Enrichment analysis: TORUS and GREGOR", "Stratified LD Score Regression", "Functional annotation integration", "Summary statistics in VCF format", "Summary statistics standardization and export", "Sample level RNA-seq quality control", "Bulk RNA-seq counts normalization", "Normalization and phenotype table generation for splicingQTL analysis", "Alternative polyadenylation", "RNA-seq expression", "Quantifying expression from RNA-seq data", "APA Calling", "Quantification of methylation data", "Quantifying alternative splicing from RNA-seq data", "Methylation", "scRNA-seq expression calling", "Alternative splicing from RNA-seq data", "eQTL summary statistics formatting", "A multivariate EBNM approach for mixture multivariate distribution estimate", "Multivariate association with MASH", "Meta-analysis with METAL", "Meta-analysis with METAL", "Illustration of xQTL protocol"], "terms": {"reproduc": [0, 38, 46], "molecular": [0, 1, 2, 5, 7, 8, 16, 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40, 42, 44, 47], "gz": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47], "tabl": [1, 2, 5, 6, 7, 11, 12, 16, 20, 22, 25, 26, 28, 31, 33, 34, 38, 40, 41, 44, 45, 48], "should": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 22, 26, 28, 32, 33, 34, 38, 40, 41, 44, 45, 50], "companion": [1, 2, 40], "tbi": [1, 2, 19, 20, 21], "format": [1, 2, 6, 8, 12, 13, 15, 16, 21, 22, 24, 25, 29, 33, 34, 35, 38, 40, 41, 44, 46, 47, 49], "genotyp": [1, 2, 4, 5, 7, 10, 16, 20, 22, 29, 34, 50], "vcf": [1, 6, 8, 10, 11, 20, 32, 38, 48, 49], "chromosom": [1, 2, 10, 11, 13, 16, 20, 22, 25, 26, 28, 32, 34, 35, 36, 39, 41], "previous": [1, 2, 7, 11, 12, 13, 16, 38, 39, 41, 47], "qc": [1, 2, 6, 20, 22, 26, 34, 35, 40, 41, 50], "pipelin": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 15, 16, 17, 19, 20, 21, 22, 23, 24, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 46, 47, 49, 50], "grm": 1, "path": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48, 50], "matric": [1, 8, 16, 21, 33, 34, 38, 40, 45, 46], "covari": [1, 2, 4, 6, 8, 12, 17, 21, 24, 33, 45, 46, 47, 50], "id": [1, 2, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 46, 50], "name": [0, 1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 28, 29, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 46, 47, 48], "colnam": [1, 2, 7, 8, 11, 12, 16, 17, 18, 21, 22, 25, 28, 31, 33, 40, 45, 46], "row": [1, 2, 5, 6, 8, 11, 12, 16, 18, 20, 21, 25, 26, 28, 31, 32, 33, 34, 35, 38, 40, 41, 42, 45, 48], "fix": [1, 2, 6, 7, 8, 9, 13, 21, 31, 32, 38, 40, 45, 48], "known": [1, 2, 9, 12, 20, 29, 40], "well": [1, 2, 6, 11, 14, 15, 20, 21, 29, 38, 40, 41, 45, 46], "hidden": [1, 2, 21, 34], "recov": [1, 2], "factor": [1, 2, 12, 18, 29, 33, 34], "sever": [1, 2, 6, 28], "summari": [1, 2, 8, 12, 21, 22, 28, 46], "statist": [1, 2, 8, 12, 13, 21, 25, 28, 38, 46], "includ": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 25, 26, 29, 32, 35, 37, 38, 41, 45, 46], "nomin": [1, 2, 32], "region": [1, 2, 4, 6, 12, 13, 17, 20, 21, 22, 25, 26, 28, 29, 31, 32, 38, 40, 48], "evid": [1, 2], "column": [1, 2, 5, 6, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 33, 34, 35, 37, 38, 39, 40, 41, 45, 48], "follow": [1, 2, 4, 5, 6, 8, 11, 13, 14, 16, 18, 19, 20, 25, 26, 28, 29, 31, 32, 33, 35, 37, 38, 39, 40, 44, 47, 50], "chrom": [1, 2, 6, 8, 10, 13, 14, 15, 17, 25, 28, 31, 32, 35, 38, 48], "po": [1, 2, 8, 13, 14, 16, 21, 22, 25, 26, 28, 31, 32, 45, 48], "posit": [1, 2, 8, 13, 21, 22, 25, 26, 28, 32, 40, 46], "basepair": [1, 2, 32], "ref": [1, 2, 3, 4, 6, 8, 12, 13, 14, 20, 22, 25, 26, 28, 29, 31, 32, 37, 38, 44, 45, 48], "refer": [1, 2, 6, 12, 13, 15, 16, 29, 32, 35, 36, 37, 38, 41, 44, 50], "allel": [1, 2, 6, 10, 11, 12, 14, 15, 25, 26, 28, 29, 31, 32, 48], "c": [1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 13, 15, 16, 17, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 35, 38, 39, 40, 41, 42, 45, 46, 47, 48], "t": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 48], "alt": [1, 2, 8, 13, 14, 20, 22, 25, 28, 31, 32, 45, 48], "trait": [1, 2, 21, 29], "identifi": [1, 2, 8, 11, 12, 15, 22, 28, 29, 31, 32, 41, 46, 50], "specifi": [1, 2, 5, 6, 7, 8, 12, 16, 17, 20, 21, 28, 38, 40, 41, 45, 46], "beta": [1, 2, 17, 21, 22, 25, 26, 29, 32, 40, 45, 48], "slope": [1, 2, 32, 45], "se": [1, 2, 5, 20, 22, 25, 26, 31, 32, 38, 41, 45, 48], "standard": [1, 2, 12, 14, 25, 26, 31, 45, 48], "error": [1, 2, 12, 22, 25, 26, 31, 32, 38, 45, 46, 48], "pval": [1, 2, 12, 22, 25, 31, 40, 45, 48], "singl": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 31, 33, 34, 35, 38, 39, 40, 41, 45], "variant_id": [1, 2, 32, 45, 48], "rsid": [1, 2, 13, 14, 20, 22, 25, 28, 32], "chr": [1, 2, 5, 6, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 34, 35, 37, 38, 39, 40, 44, 45, 48, 49], "end": [1, 2, 5, 8, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 24, 26, 29, 31, 32, 34, 35, 37, 38, 39, 40, 41, 44, 47, 48, 49], "gene_pv": 1, "calcul": [1, 2, 8, 11, 12, 13, 15, 20, 32, 33, 35, 38, 40], "across": [1, 2, 13, 32, 34, 35], "cauchi": 1, "combin": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 45], "approxim": [1, 2, 13, 20, 21], "permut": [1, 2, 32], "n_sampl": 1, "number": [1, 2, 5, 6, 7, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 44, 45, 46, 48], "n_covar": 1, "intercept": [1, 25, 29], "resid_sd": 1, "squar": [1, 14], "mean": [1, 2, 6, 7, 8, 9, 11, 12, 13, 14, 15, 18, 22, 29, 33, 35, 38, 40, 45, 46], "n_cis_vari": 1, "h": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 17, 20, 26, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "usag": [1, 2, 5, 7, 8, 10, 11, 14, 16, 18, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 45], "workflow_nam": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "target": [1, 2, 5, 6, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "workflow_opt": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "One": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "hyphen": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "see": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 26, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46], "doubl": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "lmm_null": 1, "tran": [1, 2, 32], "val": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 29, 33, 34, 35, 38, 39, 40, 41], "per": [1, 2, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 32, 33, 34, 35, 38, 40, 41, 46], "plain": 1, "leav": [1, 10, 38], "default": [1, 2, 5, 7, 8, 12, 14, 16, 19, 20, 21, 28, 32, 35, 37, 38, 39, 40, 41, 42, 45, 46, 48], "fals": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 20, 21, 22, 28, 32, 33, 35, 38, 39, 40, 41, 45, 46], "ranknorm": 1, "whether": [1, 5, 16, 22, 32, 38, 40, 46, 48], "appli": [1, 2, 6, 7, 8, 11, 12, 13, 16, 18, 22, 29, 32, 33, 38, 40, 41, 42, 46], "rank": [1, 12, 18, 33], "normal": [1, 8, 13, 33, 40, 45, 46], "cwd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47], "directori": [1, 2, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 20, 28, 31, 32, 34, 35, 38, 39, 40, 41, 45, 47], "softwar": [1, 2, 7, 8, 10, 11, 12, 13, 20, 35, 38, 40, 41], "f": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 47, 48], "phenotype_list": [1, 24], "bn": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 26, 28, 31, 32, 34, 38, 39, 40, 41, 45, 46, 48], "_": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 31, 32, 34, 35, 40, 45, 46, 48], "covariate_fil": [1, 2, 6], "1000000": [1, 2, 6, 21, 38], "int": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 17, 20, 22, 28, 32, 33, 34, 35, 38, 39, 40, 41, 45], "up": [0, 1, 2, 11, 13, 14, 21, 29, 43, 45, 46, 50], "radiu": [1, 2], "interest": [1, 2, 8, 22], "bp": [1, 2, 14, 22, 26, 29], "numthread": [1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 32, 33, 34, 35, 38, 39, 40, 41, 46], "8": [1, 2, 4, 6, 7, 8, 9, 15, 16, 19, 20, 24, 25, 33, 35, 36, 38, 39, 40, 41, 42, 45, 46], "thread": [1, 2, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 38, 39, 40, 41, 45, 46], "size": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 40, 41, 42, 45, 46, 47, 49], "walltim": [1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "5h": [1, 7, 8, 10, 11, 12, 14, 16, 17, 20, 22, 32, 33, 34, 35, 38, 40, 41, 46], "80g": [1, 21], "cis_1": [1, 2], "trans_1": [1, 2], "s_2": 1, "s_3": 1, "upload": [1, 2, 7, 8, 15, 16, 17, 24, 28, 41], "googl": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 25, 33, 34, 35, 36, 38, 41], "drive": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 25, 33, 34, 35, 36, 41], "sif": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 46, 47, 49, 50], "genotype_list": [1, 6], "vcf_list": [1, 31], "txt": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 26, 28, 31, 32, 34, 35, 36, 38, 39, 40, 41, 44, 45, 48], "recip": [1, 2, 5, 6, 38, 48], "grm_list": 1, "pca": [1, 2, 3, 4, 6, 7, 11, 21, 24, 36, 46, 47], "bicv": [1, 2], "cov": [1, 2, 6, 7, 8, 12, 33, 36, 46, 47], "outlin": [1, 15, 33, 34, 38, 40, 44, 46], "entrypoint": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 33, 34, 35, 38, 39, 40, 41, 46], "n": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 45, 46, 48], "split": [1, 2, 6, 7, 8, 10, 11, 13, 15, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "4": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 28, 32, 35, 36, 37, 39, 40, 41, 45, 46], "endswith": [1, 8, 11, 13, 16, 22, 38, 45], "els": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 26, 28, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46], "job_siz": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 32, 33, 34, 35, 38, 39, 40, 41, 46], "import": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 28, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48, 50], "panda": [1, 2, 5, 6, 8, 9, 14, 16, 17, 20, 21, 22, 28, 32, 35, 38, 41, 45, 48], "pd": [1, 2, 5, 6, 8, 9, 14, 16, 17, 20, 21, 22, 28, 32, 35, 38, 41, 45, 48], "molecular_pheno_chr_inv": [1, 35], "read_csv": [1, 2, 5, 6, 8, 9, 14, 16, 20, 21, 22, 32, 35, 38, 41, 48], "sep": [1, 2, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 20, 21, 22, 25, 28, 31, 32, 33, 35, 38, 40, 41, 45, 46, 48], "geno_chr_inv": 1, "input_inv": [1, 5, 6, 22], "merg": [1, 2, 6, 7, 8, 11, 12, 16, 20, 21, 22, 23, 26, 29, 32, 35, 38, 41, 47], "grm_chr_inv": 1, "tolist": [1, 2, 6, 8, 16, 22, 32, 35, 38, 41, 45, 48], "chr_inv": [1, 32], "x": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 48], "0": [0, 1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 31, 32, 33, 34, 36, 40, 41, 42, 45, 46, 48, 49], "file_inv": [1, 21, 32, 35, 38], "done": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 18, 19, 32, 34, 35, 39, 40, 41, 48], "precomput": 1, "store": [1, 5, 13, 20, 22], "residu": [1, 8, 9, 17, 33], "spline": 1, "term": 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40, 42, 44, 47], "gz": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47], "tabl": [1, 2, 5, 6, 7, 11, 12, 16, 20, 22, 25, 26, 28, 31, 33, 34, 38, 40, 41, 44, 45, 48], "should": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 22, 26, 28, 32, 33, 34, 38, 40, 41, 44, 45, 50], "companion": [1, 2, 40], "tbi": [1, 2, 19, 20, 21], "format": [1, 2, 6, 8, 12, 13, 15, 16, 21, 22, 24, 25, 29, 33, 34, 35, 38, 40, 41, 44, 46, 47, 49], "genotyp": [1, 2, 4, 5, 7, 10, 16, 20, 22, 29, 34, 50], "vcf": [1, 6, 8, 10, 11, 20, 32, 38, 48, 49], "chromosom": [1, 2, 10, 11, 13, 16, 20, 22, 25, 26, 28, 32, 34, 35, 36, 39, 41], "previous": [1, 2, 7, 11, 12, 13, 16, 38, 39, 41, 47], "qc": [1, 2, 6, 20, 22, 26, 34, 35, 40, 41, 50], "pipelin": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 15, 16, 17, 19, 20, 21, 22, 23, 24, 26, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 46, 47, 49, 50], "grm": 1, "path": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48, 50], "matric": [1, 8, 16, 21, 33, 34, 38, 40, 45, 46], "covari": [1, 2, 4, 6, 8, 12, 17, 21, 24, 33, 45, 46, 47, 50], "id": [1, 2, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 46, 50], "name": [0, 1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 28, 29, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 46, 47, 48], "colnam": [1, 2, 7, 8, 11, 12, 16, 17, 18, 21, 22, 25, 28, 31, 33, 40, 45, 46], "row": [1, 2, 5, 6, 8, 11, 12, 16, 18, 20, 21, 25, 26, 28, 31, 32, 33, 34, 35, 38, 40, 41, 42, 45, 48], "fix": [1, 2, 6, 7, 8, 9, 13, 21, 31, 32, 38, 40, 45, 48], "known": [1, 2, 9, 12, 20, 29, 40], "well": [1, 2, 6, 11, 14, 15, 20, 21, 29, 38, 40, 41, 45, 46], "hidden": [1, 2, 21, 34], "recov": [1, 2], "factor": [1, 2, 12, 18, 29, 33, 34], "sever": [1, 2, 6, 28], "summari": [1, 2, 8, 12, 21, 22, 28, 46], "statist": [1, 2, 8, 12, 13, 21, 25, 28, 38, 46], "includ": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 19, 20, 21, 22, 25, 26, 29, 32, 35, 37, 38, 41, 45, 46], "nomin": [1, 2, 32], "region": [1, 2, 4, 6, 12, 13, 17, 20, 21, 22, 25, 26, 28, 29, 31, 32, 38, 40, 48], "evid": [1, 2], "column": [1, 2, 5, 6, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 33, 34, 35, 37, 38, 39, 40, 41, 45, 48], "follow": [1, 2, 4, 5, 6, 8, 11, 13, 14, 16, 18, 19, 20, 25, 26, 28, 29, 31, 32, 33, 35, 37, 38, 39, 40, 44, 47, 50], "chrom": [1, 2, 6, 8, 10, 13, 14, 15, 17, 25, 28, 31, 32, 35, 38, 48], "po": [1, 2, 8, 13, 14, 16, 21, 22, 25, 26, 28, 31, 32, 45, 48], "posit": [1, 2, 8, 13, 21, 22, 25, 26, 28, 32, 40, 46], "basepair": [1, 2, 32], "ref": [1, 2, 3, 4, 6, 8, 12, 13, 14, 20, 22, 25, 26, 28, 29, 31, 32, 37, 38, 44, 45, 48], "refer": [1, 2, 6, 12, 13, 15, 16, 29, 32, 35, 36, 37, 38, 41, 44, 50], "allel": [1, 2, 6, 10, 11, 12, 14, 15, 25, 26, 28, 29, 31, 32, 48], "c": [1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 13, 15, 16, 17, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 35, 38, 39, 40, 41, 42, 45, 46, 47, 48], "t": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 48], "alt": [1, 2, 8, 13, 14, 20, 22, 25, 28, 31, 32, 45, 48], "trait": [1, 2, 21, 29], "identifi": [1, 2, 8, 11, 12, 15, 22, 28, 29, 31, 32, 41, 46, 50], "specifi": [1, 2, 5, 6, 7, 8, 12, 16, 17, 20, 21, 28, 38, 40, 41, 45, 46], "beta": [1, 2, 17, 21, 22, 25, 26, 29, 32, 40, 45, 48], "slope": [1, 2, 32, 45], "se": [1, 2, 5, 20, 22, 25, 26, 31, 32, 38, 41, 45, 48], "standard": [1, 2, 12, 14, 25, 26, 31, 45, 48], "error": [1, 2, 12, 22, 25, 26, 31, 32, 38, 45, 46, 48], "pval": [1, 2, 12, 22, 25, 31, 40, 45, 48], "singl": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 31, 33, 34, 35, 38, 39, 40, 41, 45], "variant_id": [1, 2, 32, 45, 48], "rsid": [1, 2, 13, 14, 20, 22, 25, 28, 32], "chr": [1, 2, 5, 6, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 34, 35, 37, 38, 39, 40, 44, 45, 48, 49], "end": [1, 2, 5, 8, 10, 13, 14, 16, 17, 18, 19, 20, 21, 22, 24, 26, 29, 31, 32, 34, 35, 37, 38, 39, 40, 41, 44, 47, 48, 49], "gene_pv": 1, "calcul": [1, 2, 8, 11, 12, 13, 15, 20, 32, 33, 35, 38, 40], "across": [1, 2, 13, 32, 34, 35], "cauchi": 1, "combin": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 45], "approxim": [1, 2, 13, 20, 21], "permut": [1, 2, 32], "n_sampl": 1, "number": [1, 2, 5, 6, 7, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 44, 45, 46, 48], "n_covar": 1, "intercept": [1, 25, 29], "resid_sd": 1, "squar": [1, 14], "mean": [1, 2, 6, 7, 8, 9, 11, 12, 13, 14, 15, 18, 22, 29, 33, 35, 38, 40, 45, 46], "n_cis_vari": 1, "h": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 17, 20, 26, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "usag": [1, 2, 5, 7, 8, 10, 11, 14, 16, 18, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 45], "workflow_nam": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "target": [1, 2, 5, 6, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "workflow_opt": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "One": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "hyphen": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "see": [1, 2, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 26, 28, 29, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46], "doubl": [1, 2, 5, 7, 8, 10, 11, 12, 13, 14, 16, 20, 28, 29, 33, 34, 35, 38, 39, 40, 41, 45], "lmm_null": 1, "tran": [1, 2, 32], "val": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 20, 29, 33, 34, 35, 38, 39, 40, 41], "per": [1, 2, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 32, 33, 34, 35, 38, 40, 41, 46], "plain": 1, "leav": [1, 10, 38], "default": [1, 2, 5, 7, 8, 12, 14, 16, 19, 20, 21, 28, 32, 35, 37, 38, 39, 40, 41, 42, 45, 46, 48], "fals": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 20, 21, 22, 28, 32, 33, 35, 38, 39, 40, 41, 45, 46], "ranknorm": 1, "whether": [1, 5, 16, 22, 32, 38, 40, 46, 48], "appli": [1, 2, 6, 7, 8, 11, 12, 13, 16, 18, 22, 29, 32, 33, 38, 40, 41, 42, 46], "rank": [1, 12, 18, 33], "normal": [1, 8, 13, 33, 40, 45, 46], "cwd": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47], "directori": [1, 2, 7, 8, 9, 10, 11, 12, 14, 16, 17, 18, 20, 28, 31, 32, 34, 35, 38, 39, 40, 41, 45, 47], "softwar": [1, 2, 7, 8, 10, 11, 12, 13, 20, 35, 38, 40, 41], "f": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 47, 48], "phenotype_list": [1, 24], "bn": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 26, 28, 31, 32, 34, 38, 39, 40, 41, 45, 46, 48], "_": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 25, 26, 28, 31, 32, 34, 35, 40, 45, 46, 48], "covariate_fil": [1, 2, 6], "1000000": [1, 2, 6, 21, 38], "int": [1, 2, 5, 7, 8, 10, 11, 13, 14, 16, 17, 20, 22, 28, 32, 33, 34, 35, 38, 39, 40, 41, 45], "up": [0, 1, 2, 11, 13, 14, 21, 29, 43, 45, 46, 50], "radiu": [1, 2], "interest": [1, 2, 8, 22], "bp": [1, 2, 14, 22, 26, 29], "numthread": [1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 32, 33, 34, 35, 38, 39, 40, 41, 46], "8": [1, 2, 4, 6, 7, 8, 9, 15, 16, 19, 20, 24, 25, 33, 35, 36, 38, 39, 40, 41, 42, 45, 46], "thread": [1, 2, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 38, 39, 40, 41, 45, 46], "size": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "1": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 31, 32, 33, 34, 35, 36, 40, 41, 42, 45, 46, 47, 49], "walltim": [1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "5h": [1, 7, 8, 10, 11, 12, 14, 16, 17, 20, 22, 32, 33, 34, 35, 38, 40, 41, 46], "80g": [1, 21], "cis_1": [1, 2], "trans_1": [1, 2], "s_2": 1, "s_3": 1, "upload": [1, 2, 7, 8, 15, 16, 17, 24, 28, 41], "googl": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 25, 33, 34, 35, 36, 38, 41], "drive": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 25, 33, 34, 35, 36, 41], "sif": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 46, 47, 49, 50], "genotype_list": [1, 6], "vcf_list": [1, 31], "txt": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 24, 26, 28, 31, 32, 34, 35, 36, 38, 39, 40, 41, 44, 45, 48], "recip": [1, 2, 5, 6, 38, 48], "grm_list": 1, "pca": [1, 2, 3, 4, 6, 7, 11, 21, 24, 36, 46, 47], "bicv": [1, 2], "cov": [1, 2, 6, 7, 8, 12, 33, 36, 46, 47], "outlin": [1, 15, 33, 34, 38, 40, 44, 46], "entrypoint": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 33, 34, 35, 38, 39, 40, 41, 46], "n": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 45, 46, 48], "split": [1, 2, 6, 7, 8, 10, 11, 13, 15, 16, 17, 18, 20, 21, 22, 25, 26, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48], "4": [1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 28, 32, 35, 36, 37, 39, 40, 41, 45, 46], "endswith": [1, 8, 11, 13, 16, 22, 38, 45], "els": [1, 2, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 26, 28, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46], "job_siz": [1, 2, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 32, 33, 34, 35, 38, 39, 40, 41, 46], "import": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 28, 31, 32, 33, 34, 35, 38, 39, 40, 41, 45, 46, 48, 50], "panda": [1, 2, 5, 6, 8, 9, 14, 16, 17, 20, 21, 22, 28, 32, 35, 38, 41, 45, 48], "pd": [1, 2, 5, 6, 8, 9, 14, 16, 17, 20, 21, 22, 28, 32, 35, 38, 41, 45, 48], "molecular_pheno_chr_inv": [1, 35], "read_csv": [1, 2, 5, 6, 8, 9, 14, 16, 20, 21, 22, 32, 35, 38, 41, 48], "sep": [1, 2, 5, 6, 7, 8, 9, 11, 12, 14, 16, 17, 20, 21, 22, 25, 28, 31, 32, 33, 35, 38, 40, 41, 45, 46, 48], "geno_chr_inv": 1, "input_inv": [1, 5, 6, 22], "merg": [1, 2, 6, 7, 8, 11, 12, 16, 20, 21, 22, 23, 26, 29, 32, 35, 38, 41, 47], "grm_chr_inv": 1, "tolist": [1, 2, 6, 8, 16, 22, 32, 35, 38, 41, 45, 48], "chr_inv": [1, 32], "x": [1, 2, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17, 18, 20, 21, 22, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 45, 46, 48], "0": [0, 1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 31, 32, 33, 34, 36, 40, 41, 42, 45, 46, 48, 49], "file_inv": [1, 21, 32, 35, 38], "done": [1, 2, 5, 7, 8, 11, 12, 13, 14, 16, 17, 18, 19, 32, 34, 35, 39, 40, 41, 48], "precomput": 1, "store": [1, 5, 13, 20, 22], "residu": [1, 8, 9, 17, 33], "spline": 1, "term": 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