R/replaceOutsideValues.R

In David-J-R/BEclear: Correction of batch effects in DNA methylation data

#' replaceOutsideValues
#'
#' @aliases replaceOutsideValues
#'
#' @title Replace DNA methylation values out of the boundaries
#'
#' @seealso \code{\link{findOutsideValues}}
#' @seealso \code{\link{correctBatchEffect}}
#'
#' @description A method which replaces values below 0 or beyond 1 contained in
#' the input matrix. These wrong entries are replaced by 0 or 1, respectively.
#' Note that this method is especially designed for DNA methylation data.
#'
#' @details Note that this method is especially designed to run after the batch
#' effect correction of DNA methylation data, e.g. with the
#' \code{\link{imputeMissingData}} method. It can happen, that the predicted
#' values are lying slightly below the lower bound of 0 or beyond the upper
#' bound of 1. This method finds these inaccurately predicted entries. Another
#' method called \code{\link{replaceOutsideValues}} replaces these values either
#' by 0 or 1, respectively. Another method called \code{\link{findOutsideValues}}
#' returns a list of existing wrong values and can be run before the
#' replacement.
#'
#' @param data any matrix filled with values that normally should be bounded
#' between 0 and 1.
#'
#' @export replaceOutsideValues
#' @import futile.logger
#' @usage replaceOutsideValues(data)
#'
#' @return Returns the input matrix with every value previously below 0 changed
#' to 0 and every value previously beyond 1 changed to 1.
#'
#' @examples
#' data(BEclearCorrected)
#' # Replace wrongly predicted values
#' corrected <- replaceOutsideValues(data = ex.corrected.data)
replaceOutsideValues <- function(data) {
  flog.info("Replacing values below 0 or above 1:")
  counter <- sum(data > 1) + sum(data < 0)

  data[data > 1] <- 1
  data[data < 0] <- 0
  flog.info(paste(counter, "values replaced"))

  return(data)
}