R/check_vcf.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Check if the inputted file is in VCF format
#'
#' @param header Header of the GWAS summary statistics file.
#' @return Whether the file is vcf or not
#' @keywords internal
#' @importFrom methods is
check_vcf <- function(header) {
    if (is(header, "VCFHeader")) {
        return(TRUE)
    }
    P <- LP <- INFO <- NULL
    # if the file is a VCF, first line will look like: ##fileformat=VCFv4.2
    first_line <- header[[1]]
    file_type <- gsub("^##fileformat=", "", first_line)
    is_vcf <- length(grep("^vcf", tolower(file_type))) == 1
    if (is_vcf) {
        message(
            "VCF format detected.",
            "This will be converted to a standardised table format."
        )
    }
    return(is_vcf)
}