#' 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)

}