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update method selection for NA twas results #1280

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Merged
gaow merged 1 commit into from
Jan 8, 2026
Merged

update method selection for NA twas results #1280

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27 changes: 26 additions & 1 deletion code/pecotmr_integration/twas_ctwas.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -576,6 +576,30 @@
" library(readr)\n",
"\n",
"\n",
" # function to update method selection\n",
" update_twas_method <- function(twas_df){\n",
" twas_df$method_selected_original <- twas_df$is_selected_method\n",
" twas_df_colnames <- colnames(twas_df)\n",
" twas_df$gene_context <- paste0(twas_df$molecular_id, \"_\", twas_df$context)\n",
" rs_update <- do.call(rbind, lapply(unique(twas_df$gene_context), function(gene_context){\n",
" do.call(rbind, lapply(unique(twas_df$gwas_study), function(study){\n",
" df <- twas_df[twas_df$gene_context==gene_context & twas_df$gwas_study==study,,drop=FALSE]\n",
" df_colnames <- colnames(df)\n",
" all_imputable <- df[df$rsq_cv>=${rsq_cutoff} & df$pval_cv<=${rsq_pval_cutoff} & !is.na(df$twas_z),,drop=FALSE]\n",
" if (nrow(all_imputable)<=1 || all(is.na(all_imputable$twas_z))) {\n",
" return(df) # gene-context pair does not having any other imputable model available.\n",
" } else {\n",
" message (\"Updating method selection for \", gene_context, \"-\", study, \".\")\n",
" selected_method_update <- all_imputable[order(-all_imputable$rsq_cv),]$method[1]\n",
" df$selected_method_update <- df$method==selected_method_update\n",
" df$is_selected_method <- df$selected_method_update\n",
" df <- df[, df_colnames]\n",
" return(df)\n",
" }\n",
" }))\n",
" }))\n",
" return(rs_update[, twas_df_colnames])\n",
" }\n",
"\n",
" # Load metadata and configuration - let these fail if there are issues\n",
" if (${\"TRUE\" if rename_column else \"FALSE\"}) {\n",
Expand Down Expand Up @@ -778,7 +802,8 @@
" final_results <- do.call(rbind, lapply(twas_results_db, function(x) {\n",
" if (!is.null(x$twas_result)) x$twas_result[, c(2,1,14:16,3:13)] else data.frame()\n",
" }))\n",
" \n",
" # update methods if twas z-score is NA \n",
" final_results <- update_twas_method(final_results) \n",
" message(paste(\"Writing\", nrow(final_results), \"final TWAS results\"))\n",
" fwrite(final_results, ${_output[0]:r}, sep = \"\\t\", compress = \"gzip\")\n",
" } else {\n",
Expand Down
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