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improve warning message #400

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Merged
gaow merged 1 commit into from
Jun 14, 2025
Merged

improve warning message #400

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9 changes: 6 additions & 3 deletions R/allele_qc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -83,10 +83,13 @@ allele_qc <- function(target_data, ref_variants, col_to_flip = NULL,
if (any(columns_to_remove %in% colnames(target_data))) {
target_data <- select(target_data, -any_of(columns_to_remove))
}

match_result <- merge(target_data, ref_variants, by = c("chrom", "pos"), all = FALSE, suffixes = c(".target", ".ref")) %>%
match_result <- merge(target_data, ref_variants, by = c("chrom", "pos"), all = FALSE, suffixes = c(".target", ".ref")) %>% as.data.frame()
if (nrow(match_result) == 0) {
warning("No matching variants found between target data and reference variants.")
return(list(target_data_qced = match_result, qc_summary = match_result))
}
# match target & ref by chrom and position
as.data.frame() %>%
match_result = match_result %>%
mutate(variants_id_original = paste(chrom, pos, A2.target, A1.target, sep = ":")) %>%
mutate(variants_id_qced = paste(chrom, pos, A2.ref, A1.ref, sep = ":")) %>%
# filter out totally same rows.
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7 changes: 6 additions & 1 deletion R/univariate_pipeline.R
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Expand Up @@ -200,11 +200,16 @@ rss_analysis_pipeline <- function(
if (nrow(sumstats)==0){
return(list(rss_data_analyzed = sumstats))
}

# Preprocess the input data
preprocess_results <- rss_basic_qc(sumstats, LD_data, skip_region = skip_region, remove_indels = remove_indels)
sumstats <- preprocess_results$sumstats
LD_mat <- preprocess_results$LD_mat

# Check if no variants in preprocess_results
if (nrow(sumstats)==0){
message("No variants left after preprocessing. Returning empty results.")
return(list(rss_data_analyzed = sumstats))
}
if (pip_cutoff_to_skip != 0) {
if (pip_cutoff_to_skip < 0) {
# automatically determine the cutoff to use
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