R/check_multi_rs_snp.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Ensure that SNP ids don't have multiple rs ids on one line
#'
#' @inheritParams format_sumstats
#' @param log_files list of log file locations
#' @return list containing sumstats_dt, the modified summary statistics data
#' table object and the log file list.
#' @keywords internal
#' @importFrom data.table :=
check_multi_rs_snp <- function(sumstats_dt, path, remove_multi_rs_snp,
                               imputation_ind, log_folder_ind, check_save_out,
                               tabix_index, nThread, log_files) {
    SNP <- convert_multi_rs_SNP <- NULL
    message("Checking for multiple RSIDs on one row.")
    col_headers <- names(sumstats_dt)
    # check for "rs1234;rs5678","rs1234,rs5678","rs1234_rs5678","rs1234-rs5678"
    # "rs1234-rs5678" should also deal with a space in each of the above
    if (sum("SNP" %in% col_headers) == 1 &&
        (sum(grepl("[[:punct:]]rs", sumstats_dt$SNP)) > 0) ||
        (sum(grepl("[[:punct:]] rs", sumstats_dt$SNP)) > 0)) {
        if (!remove_multi_rs_snp) { # take first
            msg <- paste0(
                formatC((sum(grepl("[[:punct:]]rs", sumstats_dt$SNP)) +
                    sum(grepl("[[:punct:]] rs", sumstats_dt$SNP))),
                big.mark = ","
                ),
                " SNPs found with ",
                "multiple RSIDs on one row, the first will be ",
                "taken. If you would rather remove these SNPs set\n",
                "`remove_multi_rs_snp=TRUE`."
            )
            message(msg)
            # if user specifies add a column to notify of the imputation
            if (imputation_ind) {
                sumstats_dt[
                    grepl("[[:punct:]]rs", SNP),
                    convert_multi_rs_SNP := TRUE
                ]
                sumstats_dt[
                    grepl("[[:punct:]] rs", SNP),
                    convert_multi_rs_SNP := TRUE
                ]
            }
            sumstats_dt[
                grepl("[[:punct:]]rs", SNP),
                SNP := gsub("([[:punct:]])rs.*", "", SNP)
            ]
            sumstats_dt[
                grepl("[[:punct:]] rs", SNP),
                SNP := gsub("([[:punct:]]) rs.*", "", SNP)
            ]
        } else { # remove rows
            msg <- paste0(
                sum(grepl("_rs", sumstats_dt$SNP)), " SNPs found with",
                " multiple RSIDs on one row, these will be ",
                "removed. If you would rather take the first RS ID ",
                "set\n`remove_multi_rs_snp`=FALSE"
            )
            # If user wants log, save it to there
            if (log_folder_ind) {
                name <- "snp_multi_rs_one_row"
                name <- get_unique_name_log_file(
                    name = name,
                    log_files = log_files
                )
                write_sumstats(
                    sumstats_dt =
                        sumstats_dt[grepl("[[:punct:]]rs", SNP) |
                            grepl("[[:punct:]] rs", SNP), ],
                    save_path =
                        paste0(
                            check_save_out$log_folder,
                            "/", name,
                            check_save_out$extension
                        ),
                    sep = check_save_out$sep,
                    #don't tab indx as could be miss values & cause err
                    #tabix_index = tabix_index,
                    nThread = nThread
                )
                log_files[[name]] <-
                    paste0(
                        check_save_out$log_folder, "/", name,
                        check_save_out$extension
                    )
            }
            message(msg)
            sumstats_dt <- sumstats_dt[!(grepl("[[:punct:]]rs", SNP) |
                grepl("[[:punct:]] rs", SNP)), ]
        }

        return(list(
            "sumstats_dt" = sumstats_dt,
            "log_files" = log_files
        ))
    } else {
        return(list(
            "sumstats_dt" = sumstats_dt,
            "log_files" = log_files
        ))
    }
}