Merge pull request #1062 from Chunmingl/main

export twas db for twas and ctwas
cumc · Sep 17, 2024 · 64eea44 · 64eea44
2 parents 7992998 + 5d84a0a
commit 64eea44
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/code/pecotmr_integration/twas.ipynb b/code/pecotmr_integration/twas.ipynb
@@ -468,14 +468,14 @@
     "        twas_result_table <- do.call(rbind, lapply(names(twas_weights_results), function(weight_db){\n",
     "          # harmonize twas weights and gwas sumstats against LD \n",
     "          twas_data_qced <- harmonize_twas(twas_weights_results[[weight_db]], LD_meta_file_path, \"${gwas_meta_data}\", \n",
-    "                                         twas_data_loader=twas_weights_loader, scale_weights=FALSE)\n",
+    "                                         twas_data_loader=twas_weights_loader)\n",
     "          gene <- names(twas_data_qced)\n",
     "          if (length(gene)<1) stop(paste0(\"No gene's data processed at harmonization process for \", weight_db, \". \"))\n",
     "          contexts <- names(twas_data_qced[[gene]][[\"weights_qced\"]])\n",
     "          twas_gene_table <- do.call(rbind, lapply(contexts, function(context){\n",
     "            twas_contexts <- do.call(rbind, lapply(gwas_studies, function(study){\n",
-    "                twas_rs <- twas_analysis(twas_data_qced[[gene]][[\"weights_qced\"]][[context]], twas_data_qced[[gene]][[\"gwas_qced\"]][[study]], \n",
-    "                                      twas_data_qced[[gene]][[\"LD\"]], rownames(twas_data_qced[[gene]][[\"weights_qced\"]][[context]]))\n",
+    "                twas_rs <- twas_analysis(twas_data_qced[[gene]][[\"weights_qced\"]][[context]][[\"weights\"]], twas_data_qced[[gene]][[\"gwas_qced\"]][[study]], \n",
+    "                                      twas_data_qced[[gene]][[\"LD\"]], rownames(twas_data_qced[[gene]][[\"weights_qced\"]][[context]][[\"weights\"]]))\n",
     "                context_table <- data.frame(gwas_study=study, method=sub(\"_[^_]+$\", \"\",names(twas_rs)), twas_z=find_data(twas_rs, c(2, \"z\")),\n",
     "                                        twas_pval=find_data(twas_rs, c(2, \"pval\")))\n",
     "                return(context_table)\n",
@@ -505,7 +505,7 @@
     "          cv_rsqs <- sapply(cv_data[[context]], function(x) x[, \"rsq\"])\n",
     "          cv_pvals <- sapply(cv_data[[context]], function(x) x[, \"pval\"])\n",
     "          context_table <- data.frame(context=context, method=methods, is_imputable = is_imputable, is_selected_method=is_selected_method,\n",
-    "                                    rsq_cv=cv_rsqs, pval_cv=cv_pvals)\n",
+    "                                    rsq_cv=cv_rsqs, pval_cv=cv_pvals, type=export_twas_weights_db[[\"${_filtered_region_info[3]}\"]][[gene]][[context]]$data_type)\n",
     "          return(context_table)\n",
     "        }))\n",
     "        gene_table$gene = gene\n",