--- a
+++ b/R/PrepWilcoxon.R
@@ -0,0 +1,48 @@
+#' Prepare Wilcoxon DEG data for plotting
+#'
+#' This function reads a Wilcoxon DEG data frame from an RDS file, filters it using
+#' \code{\link{deg_filter}} function, adjusts the log2foldChange to absolute values, adds a pseudo-count to pValues,
+#' and transforms pValues for plotting. The final data frame is returned and
+#' optionally saved to a new RDS file.
+#'
+#' @param input_path Path to the RDS file containing the Wilcoxon DEG data frame.
+#' @param output_name Optional; name for the processed data frame, also used as the RDS file name.
+#'        If not provided, the data frame will not be saved to file.
+#' @return A data frame with processed Wilcoxon DEG data.
+#' @export
+#' @examples
+#' wilcoxon_file <- system.file("extdata",
+#'                              "Wilcoxon_rank_sum_testoutRst_test.rds",
+#'                              package = "TransProR")
+#' Wilcoxon <- prep_wilcoxon(wilcoxon_file)
+#'
+prep_wilcoxon <- function(input_path, output_name = NULL) {
+  # Read the Wilcoxon DEG data frame from an RDS file
+  Wilcoxon <- readRDS(input_path)
+
+  # Filter DEG data using the deg_filter function from the same package
+  Wilcoxon_filter <- deg_filter(Wilcoxon)
+  Wilcoxon <- Wilcoxon[rownames(Wilcoxon) %in% Wilcoxon_filter, ]
+
+  # Select columns of interest and adjust log2foldChange values to absolute values
+  Wilcoxon <- Wilcoxon[, c('log2foldChange', "pValues", "change")]
+  Wilcoxon$log2foldChange <- abs(Wilcoxon$log2foldChange)
+
+  # Add a small pseudo-count to pValues to avoid log of zero and transform pValues for plotting
+  Wilcoxon$pValues <- Wilcoxon$pValues + .Machine$double.eps
+  Wilcoxon$pValues <- -log10(Wilcoxon$pValues)
+
+  # Extract the Gene column from row names
+  Wilcoxon$Gene <- rownames(Wilcoxon)
+
+  # Rename columns
+  names(Wilcoxon) <- c('logFC', 'Pvalue', "change", 'Gene')
+
+  # Optionally save the processed data frame as an RDS file
+  if (!is.null(output_name) && nzchar(output_name)) {
+    saveRDS(Wilcoxon, paste0(output_name, ".Rdata"))
+  }
+
+  # Return the processed data frame
+  return(Wilcoxon)
+}