From fd566143215e6c576b44f8a0cef7400015769291 Mon Sep 17 00:00:00 2001 From: Chunmingl Date: Wed, 25 Sep 2024 01:31:59 -0400 Subject: [PATCH] minor fix --- code/pecotmr_integration/twas.ipynb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/code/pecotmr_integration/twas.ipynb b/code/pecotmr_integration/twas.ipynb index fa058acc..9d75dba3 100644 --- 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",