R/check_two_step_col.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Ensure that CHR:BP aren't merged into 1 column
#'
#' @param sumstats_dt data table obj of the summary statistics
#'  file for the GWAS
#' @param path Filepath for the summary statistics file to be formatted
#' @returns list containing sumstats_dt, the modified summary
#'  statistics data table object
#' @keywords internal
#' @importFrom data.table tstrsplit
#' @importFrom data.table :=
check_two_step_col <- function(sumstats_dt, path) {
    # get col headers
    col_headers <- names(sumstats_dt)
    # Obtain a row of the actual data
    row_of_data <- as.character(sumstats_dt[1, ])
    twoStepCol <- grep(".*:.*", row_of_data)
    # in case there are more than one column with ":", just take first one
    if (length(twoStepCol) > 1) {
        # sort to get most recent genome build by 
        # default (cols: SNP_hg19, SNP_hg18)
        keep_col <- sort(col_headers[twoStepCol], decreasing = TRUE)[1]
        drop_cols <- sort(col_headers[twoStepCol], decreasing = TRUE)[-1]
        msg <- paste0(
            "Warning: Multiple columns in the sumstats file seem to ",
            "relate to Chromosome:Base Pair position.\nThe column ",
            keep_col, " will be kept whereas the column(s) ",
            drop_cols, " will be removed.\nIf this is not the correct ",
            "column to keep, please remove all incorrect columns from ",
            "those listed here before \nrunning `format_sumstats()`."
        )
        message(msg)
        # Get data without dropped
        sumstats_dt[, (drop_cols) := NULL]
        twoStepCol <- which(col_headers == keep_col)
    }
    if (length(twoStepCol)) {
        keep_col <- col_headers[twoStepCol]
        # split out col into separate values, keep names
        format <- strsplit(keep_col, ":")[[1]]
        if (length(format) != 2) { # check : and underscore in name
            format <- strsplit(keep_col, "_")[[1]]
        }
        if (length(format) != 2) { # If neither found assign name
            format <- c("CHR", "BP")
        }
        # keep ensures that even if certain rows have 3 values
        # e.g.16:23609681:ID
        # only first two taken
        sumstats_dt[, (format) := data.table::tstrsplit(get(keep_col),
            split = ":", fixed = TRUE,
            keep = c(1, 2),
            type.convert = TRUE
        )]
        # remove combined column
        sumstats_dt[, (keep_col) := NULL]
        msg <- paste0(
            "Column ", keep_col, " has been separated into the columns ",
            paste(format, collapse = ", ")
        )
        message(msg)

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