R/subSetNA.R

In MolecularPathologyLab/MmCMS: Calling CMS for mouse tissue

#' sets NTP results to NA based on p-value cutoff
#' @description sets \code{ntp} predictions to NA based on \eqn{p}-value or FDR
#' thresholds
#' @param res a data frame, result from \code{\link{ntp}} function.
#' @param pValue a numeric, predictions with higher p-values are set to NA.
#' @param FDR a numeric, predictions with higher FDR are set to NA.
#' @param verbose logical, whether console messages are to be displayed.
#' @details Replaces low-confidence predictions with NA.
#' @return A data.frame where res$prediction's are set to NA based on
#' \eqn{p}-value or FDR threshold.
subSetNA <- function(res, pValue = 1, FDR = 1, verbose = TRUE)
{

  # checkInput #####
  if(is.null(res$prediction) | is.null(res$p.value) | is.null(res$FDR))
  { stop("error in res, check input") }

  # reset in case of prior resets
  classN <- levels(res$prediction)
  isDist <- grepl("d\\.", colnames(res))
  res$prediction <- classN[apply(res[,isDist], 1, which.min)]
  res$prediction <- factor(res$prediction, levels = classN)

  # process #####
  setNA <- res$p.value > pValue | res$FDR > FDR
  res$prediction[setNA] <- NA
  if (isTRUE(verbose))
    message(paste0(sum(setNA), "/", nrow(res), " samples set to NA"))
  # returnOutput #####
  return(res)
}