R/check_vital_col.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Ensure that all necessary columns are in the summary statistics file
#'
#' @param sumstats_dt data table obj of the summary statistics file for the GWAS
#' @return null
#' @keywords internal
check_vital_col <- function(sumstats_dt) {
    col_headers <- names(sumstats_dt)
    err_msg <-
        paste("Cannot find a %s column in GWAS sumstats.",
              "\nUse code such as '%s' to fix")
    for (key_column in c("SNP", "CHR", "BP", "P", "A1", "A2")) {
        code_example <- "sed -i '' '1s/p_value/P/' IQ.Sniekers.2017.txt"
        if (!key_column %in% col_headers) {
            stop(sprintf(err_msg, key_column, code_example))
        }
    }
}