R/function_proc_data.R

In PaoloBnn/Retip: Retention Time Prediction for Metabolomics

#' Clean dataset removing NA value and Near zero variance columns.
#' @export proc.data
#' @param x A dataset with calculated Chemical Descriptors.
#' @return  Returns cleaned up dataset removing column with NA value and Near
#' zero variance.
#' @examples
#' \donttest{
#' # descs is a previusly dataset with calculate chemical descriptors from
#' function getCD
#' db_rt <- proc.data(descs)}



proc.data  <- function(x) {
  # remove na columns
  db <- x[, !apply(x, 2, function(x) any(is.na(x)))]

  set.seed(101)

  # remove columns with near zero variance values
  nzvColumns <- caret::nearZeroVar(db)

  mdrDescFH <- db[, -nzvColumns]

  db_rt <- data.frame(mdrDescFH[, -c(1:3)])

  return(db_rt)

}