R/readSNPTESTsamplefileASdata_table.R

In holgerman/toolboxH: Helperfunctions for R

## read SNPTEST sample file in R as data.table
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param snptest_sample_fn PARAM_DESCRIPTION
#' @param makeBinaryOutcomeNumeric12 PARAM_DESCRIPTION, Default: T
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#'  #EXAMPLE1
#'  }
#' }
#' @rdname readSNPTESTsamplefileASdata.table
#' @export
readSNPTESTsamplefileASdata.table <- function (snptest_sample_fn, makeBinaryOutcomeNumeric12 = T) {

  samplefile = data.table::fread(snptest_sample_fn)

  samplefile_types = unlist(samplefile[1])
  samplefile_types
  samplefile = samplefile[-1]

  for(i in names(samplefile_types[samplefile_types %in% c("C","P")])) {
    samplefile[,(i) := as.numeric(get(i))]
  }

  for(i in names(samplefile_types[samplefile_types %in% c("D","B")])) {
    samplefile[,(i) := factor(get(i))]
  }


  ## binary in 1 2 recodieren
  if(makeBinaryOutcomeNumeric12 == T) {for(i in names(samplefile_types[samplefile_types %in% c("B")])) {

    samplefile[,(i) := as.numeric(factor(get(i)))]
    samplefile[,if(any(stats::na.omit(get(i)) %nin% c(1,2))) stop(paste0("Case/control phenotype " ,i, " is not encoded in exactly two levels...")) ]

  }}

  # str(samplefile)
  samplefile
}