minor fix

cumc · Sep 25, 2024 · fd56614 · fd56614
1 parent 8894e68
commit fd56614
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/code/pecotmr_integration/twas.ipynb b/code/pecotmr_integration/twas.ipynb
@@ -408,8 +408,7 @@
     "        filtered_regional_xqtl_files.append(files)\n",
     "    else:\n",
     "        skipped_regions.append(region)\n",
-    "print(f\"Skipping {len(skipped_regions)} out of {len(regional_xqtl_files)} regions, no overlapping xQTL weights found. \")\n",
-    "#sos_variable(\"filtered_region_info\", filtered_region_info)"
+    "print(f\"Skipping {len(skipped_regions)} out of {len(regional_xqtl_files)} regions, no overlapping xQTL weights found. \")"
    ]
   },
   {
@@ -532,7 +531,7 @@
     "    library(ctwas) # multigroup_ctwas\n",
     "    library(pecotmr)\n",
     "\n",
-    "    regions_data <- get_ctwas_meta_data(\"${ld_meta_data}\", \"${regions}\")\n",
+    "    regions_data <- get_ctwas_meta_data(\"${ld_meta_data}\", \"${regions}\", \"${xqtl_meta_data}\")\n",
     "    gwas_studies <- unique(fread(\"${gwas_meta_data}\",data.table=FALSE, select = \"study_id\"))[,1]\n",
     "\n",
     "    data <- lapply(c(${_input:r,}), readRDS)\n",
@@ -570,7 +569,7 @@
     "                                logfile = file.path(${_output[0]:dr}, paste0(\"${name}\", \".ctwas_sumstats.log\")),\n",
     "                                verbose = FALSE, \n",
     "                                cor_dir = NULL,\n",
-    "                                save_cor = TRUE,\n",
+    "                                save_cor = FALSE,\n",
     "                                group_prior_var_structure = c(\"shared_context\"),\n",
     "                                LD_format=\"custom\", \n",
     "                                LD_loader_fun = ctwas_ld_loader,\n",