R/standardise.sumstats.column.headers.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Standardise the column headers in the Summary Statistics files
#'
#' Use a reference data table of common column header names
#'  (stored as \code{MAGMA.Celltyping::sumstatsColHeaders}) 
#'  convert them to a standard set, i.e. chromosome --> CHR.
#' This function does not check that all the required column headers
#'  are present.
#' The amended header is written directly back into the file.
#'
#' @param path File path for the summary statistics file.
#'
#' @returns The amended column headers 
#' (also the column headers will be written directly 
#' into the summary statistics file)
#'
#' @examples
#' \dontrun{ 
#' path <- MAGMA.Celltyping::get_example_gwas()
#' col_headers <- MAGMA.Celltyping::standardise.sumstats.column.headers(
#'     path = path)
#' }
#' @export
standardise.sumstats.column.headers <- function(path) {
    .Deprecated("MungeSumstats::format_sumstats")
    mungesumstats_deprecation_msg()
}