Merge pull request #1058 from Chunmingl/main

minor fix - bring back bayes"_r"

code/pecotmr_integration/twas.ipynb

@@ -424,7 +424,7 @@
     "    library(IRanges)\n",
     "    library(R6)\n",
     "    library(pecotmr)\n",
-    "  \n",
+    "    \n",
     "    LD_meta_file_path = \"${ld_meta_data}\"\n",
     "    region_block <- unlist(strsplit(\"${_filtered_region_info[3]}\", \"_\\\\s*\"))\n",
     "    chrom = as.integer(gsub(\"chr\", \"\", region_block[1]))\n",
@@ -452,7 +452,7 @@
     "        weight_dbs <- weight_db_list_update[[gene_db]]\n",
     "        twas_weights_results[[gene_db]] = generate_twas_db(weight_dbs, contexts=NULL,variable_name_obj=c(\"variant_names\"), susie_obj=\"susie_weights_intermediate\",\n",
     "                                         twas_weights_table = \"twas_weights\", min_rsq_threshold = ${rsq_threshold}, \n",
-    "                                         p_val_cutoff = ${p_value_cutoff}, data_type_table=xqtl_type_table)\n",
+    "                                         p_val_cutoff = ${p_value_cutoff}, data_type_table=xqtl_type_table, region_name=gene_db)\n",
     "        if (gene_db %in% names(twas_weights_results)){\n",
     "            # merge and update export_twas_weights_db for imputable genes, merge if same gene's other context results are available \n",
     "            if (!is.null(twas_weights_results[[gene_db]])){\n",
@@ -476,7 +476,7 @@
     "            twas_contexts <- do.call(rbind, lapply(gwas_studies, function(study){\n",
     "                twas_rs <- twas_analysis(twas_data_qced[[gene]][[\"weights_qced\"]][[context]], twas_data_qced[[gene]][[\"gwas_qced\"]][[study]], \n",
     "                                      twas_data_qced[[gene]][[\"LD\"]], rownames(twas_data_qced[[gene]][[\"weights_qced\"]][[context]]))\n",
-    "                context_table <- data.frame(gwas_study=study, method=gsub( \"_.*$\", \"\",names(twas_rs)), twas_z=find_data(twas_rs, c(2, \"z\")),\n",
+    "                context_table <- data.frame(gwas_study=study, method=sub(\"_[^_]+$\", \"\",names(twas_rs)), twas_z=find_data(twas_rs, c(2, \"z\")),\n",
     "                                        twas_pval=find_data(twas_rs, c(2, \"pval\")))\n",
     "                return(context_table)\n",
     "            }))\n",
@@ -497,7 +497,7 @@
     "                          function(file){if(twas_weights_results[[file]]$gene == gene) twas_weights_results[[file]]$cv_performance}))\n",
     "        # loop through each context for all methods\n",
     "        gene_table <- do.call(rbind, lapply(contexts, function(context){\n",
-    "          methods <- gsub(\"_.*$\", \"\", names(cv_data[[context]]))\n",
+    "          methods <- sub(\"_[^_]+$\", \"\",names(cv_data[[context]]))\n",
     "          is_imputable = export_twas_weights_db[[\"${_filtered_region_info[3]}\"]][[gene]][[context]]$is_imputable\n",
     "          selected_method = export_twas_weights_db[[\"${_filtered_region_info[3]}\"]][[gene]][[context]]$selected_model\n",
     "          if(is.null(selected_method)) selected_method <- NA\n",