--- a
+++ b/R/DIscBIO-generic-FinalPreprocessing.R
@@ -0,0 +1,75 @@
+#' @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)
+  }
+)