--- a
+++ b/man/prep_deseq2.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PrepDeseq2.R
+\name{prep_deseq2}
+\alias{prep_deseq2}
+\title{Prepare DESeq2 data for plotting}
+\usage{
+prep_deseq2(input_path, output_name = NULL)
+}
+\arguments{
+\item{input_path}{Path to the RDS file containing the DESeq2 DEG data frame.}
+
+\item{output_name}{Name for the processed data frame, also used as the RDS file name.}
+}
+\value{
+A data frame with processed DESeq2 DEG data.
+}
+\description{
+This function reads a DESeq2 DEG data frame from an RDS file, filters it,
+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.
+}
+\examples{
+deseq2_file <- system.file("extdata",
+                           "DEG_deseq2_test.rds",
+                           package = "TransProR")
+deseq2 <- prep_deseq2(deseq2_file)
+
+}