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minor fix in tensorqtl postprocessor #392

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Merged
gaow merged 1 commit into from
May 20, 2025
Merged

minor fix in tensorqtl postprocessor #392

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9 changes: 5 additions & 4 deletions inst/code/tensorqtl_postprocessor.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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$end_distance_col)
col_indices <- sapply(required_cols, function(col) which(all_cols == col))
if (any(sapply(col_indices, length) == 0)) {
stop(sprintf("Required columns missing in file: %s", filename))
Expand Down Expand Up @@ -349,7 +348,9 @@ calculate_filtered_variant_counts <- function(filename, params, gene_coords) {
qtl_data,
params$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...")
Expand Down Expand Up @@ -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),
Expand Down
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