From bd27019825d5f4e7168b81e1fd3e5be1ee880393 Mon Sep 17 00:00:00 2001 From: Anjing Date: Tue, 20 May 2025 16:22:24 -0400 Subject: [PATCH] minor fix: adding start_distance_col, end_distance_col in calculate_feature_positions() calling --- inst/code/tensorqtl_postprocessor.R | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/inst/code/tensorqtl_postprocessor.R b/inst/code/tensorqtl_postprocessor.R index 5395e241..5fee5fae 100644 --- a/inst/code/tensorqtl_postprocessor.R +++ b/inst/code/tensorqtl_postprocessor.R @@ -314,8 +314,7 @@ calculate_filtered_variant_counts <- function(filename, params, gene_coords) { molecular_id_col <- params$molecular_id_col %||% "molecular_trait_object_id" message(sprintf("Counting per event variants in %s", basename(filename))) all_cols <- extract_column_names(filename, params$pvalue_pattern, params$qvalue_pattern)$all_columns - required_cols <- c(molecular_id_col, "chrom", "pos", params$af_col) - + required_cols <- c(molecular_id_col, "chrom", "pos", params$af_col, params$start_distance_col, params$end_distance_col) col_indices <- sapply(required_cols, function(col) which(all_cols == col)) if (any(sapply(col_indices, length) == 0)) { stop(sprintf("Required columns missing in file: %s", filename)) @@ -349,7 +348,9 @@ calculate_filtered_variant_counts <- function(filename, params, gene_coords) { qtl_data, params$cis_window, gene_coords, - molecular_id_col + molecular_id_col, + params$start_distance_col, + params$end_distance_col ) message("Applying MAF and cis-window filters...") @@ -547,7 +548,7 @@ prepare_local_qtl_data <- function(qtl_data, regional_data, params, should_filte filter(pmin(!!sym(params$af_col), 1 - !!sym(params$af_col)) > params$maf_cutoff) } else { # Original logic: apply both cis-window and MAF filtering - feature_positions <- calculate_feature_positions(qtl_data$data, params$cis_window, qtl_data$gene_coords, molecular_id_col) + feature_positions <- calculate_feature_positions(qtl_data$data, params$cis_window, qtl_data$gene_coords, molecular_id_col, params$start_distance_col, params$end_distance_col) filtered_data <- qtl_data$data %>% left_join( feature_positions %>% select(!!sym(molecular_id_col), cis_start, cis_end),