--- a
+++ b/R/PrepEdgeR.R
@@ -0,0 +1,47 @@
+#' Prepare edgeR DEG data for plotting
+#'
+#' This function reads an edgeR DEG data frame from an RDS file, filters it using
+#' \code{\link{deg_filter}} function, adjusts the logFC to absolute values, adds a pseudo-count to PValue,
+#' and transforms PValue 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 edgeR DEG data frame.
+#' @param output_name Name for the processed data frame, also used as the RDS file name.
+#' @return A data frame with processed edgeR DEG data.
+#' @export
+#' @examples
+#' edgeR_file <- system.file("extdata",
+#'                           "DEG_edgeR_test.rds",
+#'                           package = "TransProR")
+#' edgeR <- prep_edgeR(edgeR_file)
+#'
+prep_edgeR <- function(input_path, output_name = NULL) {
+  # Read the edgeR DEG data frame from an RDS file
+  DEG_edgeR <- readRDS(input_path)
+
+  # Filter DEG data using the deg_filter function from the same package
+  edgeR <- deg_filter(DEG_edgeR)
+  DEG_edgeR <- DEG_edgeR[rownames(DEG_edgeR) %in% edgeR, ]
+
+  # Select columns of interest and adjust logFC values to absolute values
+  DEG_edgeR <- DEG_edgeR[, c('logFC', "PValue", "change")]
+  DEG_edgeR$logFC <- abs(DEG_edgeR$logFC)
+
+  # Add a small pseudo-count to PValue to avoid log of zero and transform PValue for plotting
+  DEG_edgeR$PValue <- DEG_edgeR$PValue + .Machine$double.eps
+  DEG_edgeR$PValue <- -log10(DEG_edgeR$PValue)
+
+  # Extract the Gene column from row names
+  DEG_edgeR$Gene <- rownames(DEG_edgeR)
+
+  # Rename columns
+  names(DEG_edgeR) <- c('logFC', 'Pvalue', "change", 'Gene')
+
+  # Optionally save the processed data frame as an RDS file
+  if (!is.null(output_name)) {
+    saveRDS(DEG_edgeR, paste0(output_name, ".Rdata"))
+  }
+
+  # Return the processed data frame
+  return(DEG_edgeR)
+}