R/DIscBIO-generic-FinalPreprocessing.R

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

#' @title Final Preprocessing
#' @description This function generates the final filtered normalized dataset.
#' @param object \code{DISCBIO} class object.
#' @param GeneFlitering GeneFlitering has to be one of the followings:
#'   ["NoiseF","ExpF"]. Default is "NoiseF"
#' @param export A logical vector that allows writing the final gene list in
#'   excel file. Default is TRUE.
#' @param quiet if `TRUE`, intermediary output is suppressed
#' @param fileName File name for exporting (if `export = TRUE`)
#' @return The DISCBIO-class object input with the FinalGeneList slot filled.
#' @examples
#' #sc <- DISCBIO(valuesG1msTest)
#' #sc <- NoiseFiltering(sc, percentile = 0.9, CV = 0.2, export = FALSE)
#' #sc <- FinalPreprocessing(sc, GeneFlitering = "NoiseF", export = FALSE)
#'
setGeneric(
  "FinalPreprocessing",
  function(object,
           GeneFlitering = "NoiseF",
           export = FALSE,
           quiet = FALSE,
           fileName = "filteredDataset") {
    standardGeneric("FinalPreprocessing")
  }
)

#' @export
#' @rdname FinalPreprocessing
setMethod(
  "FinalPreprocessing",
  signature = "DISCBIO",
  definition = function(object, GeneFlitering, export, quiet, fileName) {
    if (GeneFlitering == "NoiseF") {
      if (length(object@noiseF) < 1) {
        stop("run NoiseFiltering before running FinalPreprocessing")
      }
      if (nrow(object@fdata) < 1) {
        stop("run Normalizedata before running FinalPreprocessing")
      }
      gene_list <- object@noiseF
      gene_names <- rownames(object@fdata)
      idx_genes <- is.element(gene_names, gene_list)
      gene_names2 <- gene_names[idx_genes]
      filteredDataset <- object@fdata[gene_names2, ]
      object@fdata <- filteredDataset
      object@FinalGeneList <- rownames(filteredDataset)
    }
    if (GeneFlitering == "ExpF") {
      if (nrow(object@fdata) < 1) {
        stop("run Normalizedata before running FinalPreprocessing")
      }
      filteredDataset <- object@fdata
      object@FinalGeneList <- rownames(filteredDataset)
    }
    if (!quiet) {
      message(
        "The gene filtering method = Noise filtering\n\n",
        "The Filtered Normalized dataset contains:\n",
        "Genes: ", length(filteredDataset[, 1]), "\n",
        "cells: ", length(filteredDataset[1, ]), "\n\n"
      )
    }
    if (export) {
      fileNameExt <- paste0(fileName, ".Rdata")
      if (!quiet) {
        message(
          "The Filtered Normalized dataset was saved as: ",
          fileNameExt
        )
      }
      save(filteredDataset, file = fileNameExt)
    }
    return(object)
  }
)