Fixing column standardisation for OR, hopefully for good (#158)

Author: andrew-e

pipeline_steps/common_extraction_functions.R

@@ -169,17 +169,14 @@ use_bed_file_to_update_gwas <- function(gwas, bed_file) {
   return(gwas)
 }
 
-standardise_columns <- function(gwas, N) {
+standardise_columns <- function(gwas) {
   gwas_columns <- colnames(gwas)
 
-  if (!all(c("CHR", "BP") %in% gwas_columns)) {
-    if (all(grepl("\\d:\\d", gwas$SNP))) {
-      gwas <- tidyr::separate(data = gwas, col = "SNP", into = c("CHR", "BP"), sep = "[:_]", remove = F)
-      gwas$BP <- as.numeric(gwas$BP)
-    }
-  }
+  chr_numeric <- suppressWarnings(as.numeric(gsub("^chr", "", as.character(gwas$CHR))))
+  gwas <- gwas[chr_numeric %in% 1:22, ]
+  gwas$CHR <- chr_numeric[chr_numeric %in% 1:22]
 
-  if (all(c("OR", "OR_LB", "OR_UB") %in% gwas_columns) && !all(c("BETA", "SE") %in% colnames(gwas))) {
+  if (all(c("OR", "OR_LB", "OR_UB") %in% gwas_columns) && !all(c("BETA", "SE") %in% gwas_columns)) {
     gwas <- convert_or_to_beta(gwas)
   }
 
@@ -191,21 +188,15 @@ standardise_columns <- function(gwas, N) {
     gwas <- convert_z_score_to_beta(gwas)
   }
 
-  if ("BP" %in% gwas_columns) gwas$BP <- as.numeric(gwas$BP)
-  if ("P" %in% gwas_columns) {
-    gwas$P <- as.numeric(gwas$P)
-    gwas$P[gwas$P == 0] <- .Machine$double.xmin
-  }
-  if ("BETA" %in% gwas_columns) {
-    gwas$BETA <- as.numeric(gwas$BETA)
-  }
-
-  if ("BETA" %in% gwas_columns) {
-    gwas$BETA <- as.numeric(gwas$BETA)
-  }
+  gwas$BP <- as.numeric(gwas$BP)
+  gwas$BETA <- as.numeric(gwas$BETA)
+  gwas$P <- as.numeric(gwas$P)
+  gwas$P[gwas$P == 0] <- .Machine$double.xmin
 
   return(gwas)
 }
+
+
 standardise_alleles <- function(gwas) {
   gwas$EA <- toupper(gwas$EA)
   gwas$OA <- toupper(gwas$OA)
@@ -343,7 +334,6 @@ split_into_regions <- function(gwas, ld_blocks, study_metadata, p_value_threshol
 #' @import stats
 #' @export
 convert_or_to_beta <- function(gwas) {
-  gwas <- get_file_or_dataframe(gwas)
   if (!all(c("OR", "OR_LB", "OR_UB") %in% colnames(gwas))) {
     stop("Need OR, OR_LB + OR_UB to complete conversion")
   }

pipeline_steps/extract_regions_from_summary_stats.R

@@ -44,11 +44,7 @@ main <- function() {
     gwas <- vroom::vroom(study_metadata$file_location, show_col_types = F)
     study_metadata$column_names <- Filter(\(column) !is.null(column) && !is.na(column), study_metadata$column_names)
     gwas <- change_column_names(gwas, study_metadata$column_names)
-
-    # Filter out rows with non-numeric CHR (e.g. chrX, chr7_KI270803v1_alt) and convert to numeric
-    chr_numeric <- suppressWarnings(as.numeric(gsub("^chr", "", as.character(gwas$CHR))))
-    gwas <- gwas[chr_numeric %in% 1:22, ]
-    gwas$CHR <- chr_numeric[chr_numeric %in% 1:22]
+    gwas <- standardise_columns(gwas)
 
     start_time <- Sys.time()
     if (study_metadata$reference_build != reference_builds$GRCh38) {

tests/testing_complete.txt

@@ -1 +1 @@
-SUCCESS: All tests passed on branch: bug/pipeline-gwas-with-or
+SUCCESS: All tests passed on branch: bug/extract-standardise-columns

worker/pipeline_worker.R

@@ -182,9 +182,6 @@ process_message <- function(original_gwas_info, original_payload = NULL) {
         vroom::vroom_write(gwas, gwas_info$metadata$file_location)
         flog.info(paste(gwas_info$metadata$guid, "Added EAF column (NA) for LD panel fill-in during standardisation"))
       }
-      if (all(or_columns %in% colnames(updated_gwas)) && !all(beta_columns %in% colnames(updated_gwas))) {
-        updated_gwas <- convert_or_to_beta(updated_gwas)
-      }
 
       flog.info(paste(gwas_info$metadata$guid, "Extracting regions"))
       extract_regions <- glue::glue(