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minor fix for harmonization #397

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Merged
gaow merged 1 commit into from
Jun 3, 2025
Merged

minor fix for harmonization #397

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3 changes: 2 additions & 1 deletion R/twas.R
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Original file line number Diff line number Diff line change
Expand Up @@ -251,7 +251,8 @@ harmonize_gwas <- function(gwas_file, query_region, ld_variants, col_to_flip=NUL
if(is.null(gwas_file)| is.na(gwas_file)) stop("No GWAS file path provided. ")
gwas_data_sumstats <- as.data.frame(tabix_region(gwas_file, query_region)) # extension for yml file for column name mapping
if (nrow(gwas_data_sumstats) == 0) {
warning(paste0("No GWAS summary statistics found for the region of ", query_region, " in ", study, ". "))
if (length(names(gwas_file))==0) names(gwas_file) <- gwas_file
warning(paste0("No GWAS summary statistics found for the region of ", query_region, " in ", names(gwas_file), ". "))
return(NULL)
}
if (colnames(gwas_data_sumstats)[1] == "#chrom") colnames(gwas_data_sumstats)[1] <- "chrom" # colname update for tabix
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