R/leadSNP_comparison.R

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

leadSNP_comparison <- function(top_SNPs,
                               merged_results) {
    
    leadSNP <- finemappedSNP <- Overlap <- SNP <- Gene <- NULL;
        leadSNP_summary_table <- data.table::merge.data.table(
            x = top_SNPs |> 
                dplyr::select(leadSNP = SNP, Gene) |> 
                data.table::data.table(),
            y = merged_results |> 
                dplyr::select(finemappedSNP = SNP, Gene) |>
                data.table::data.table(),
            by = "Gene", all = TRUE
        ) |>
        dplyr::group_by(Gene, leadSNP) |>
        dplyr::mutate(Overlap = leadSNP %in% finemappedSNP) |>
        dplyr::group_by(Gene) |>
        dplyr::summarise(Overlap = sum(Overlap)) |>
        dplyr::mutate(leadSNP_in_CredSet = Overlap > 0)

    percent_leadSNPs <- round(
        sum(leadSNP_summary_table$leadSNP_in_CredSet) /
            length(leadSNP_summary_table$leadSNP_in_CredSet) * 100, 2
    )
    return(leadSNP_summary_table[, c("Gene", "leadSNP_in_CredSet")])
}