--- a
+++ b/man/limma_analyze.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/LimmaAnalyze.R
+\name{limma_analyze}
+\alias{limma_analyze}
+\title{Differential Gene Expression Analysis using limma and voom}
+\usage{
+limma_analyze(
+  tumor_file,
+  normal_file,
+  output_file,
+  logFC_threshold = 2.5,
+  p_value_threshold = 0.01
+)
+}
+\arguments{
+\item{tumor_file}{Path to the tumor data file (RDS format).}
+
+\item{normal_file}{Path to the normal data file (RDS format).}
+
+\item{output_file}{Path to save the output DEG data (RDS format).}
+
+\item{logFC_threshold}{Threshold for log fold change for marking up/down-regulated genes.}
+
+\item{p_value_threshold}{Threshold for p-value for filtering significant genes.}
+}
+\value{
+A data frame of differential expression results.
+}
+\description{
+This function performs differential gene expression analysis using the 'limma' package with voom normalization.
+It reads tumor and normal expression data, merges them, filters low-expressed genes,
+normalizes the data, performs limma analysis, and outputs the results along with information
+on gene expression changes.
+}
+\examples{
+# Define file paths for tumor and normal data from the data folder
+tumor_file <- system.file("extdata",
+                          "removebatch_SKCM_Skin_TCGA_exp_tumor_test.rds",
+                          package = "TransProR")
+normal_file <- system.file("extdata",
+                           "removebatch_SKCM_Skin_Normal_TCGA_GTEX_count_test.rds",
+                           package = "TransProR")
+output_file <- file.path(tempdir(), "DEG_limma_voom.rds")
+
+DEG_limma_voom <- limma_analyze(
+  tumor_file = tumor_file,
+  normal_file = normal_file,
+  output_file = output_file,
+  logFC_threshold = 2.5,
+  p_value_threshold = 0.01
+)
+
+# View the top 5 rows of the result
+head(DEG_limma_voom, 5)
+}
+\references{
+limma:Linear Models for Microarray and RNA-Seq Data User’s Guide.
+For more information, visit the page:
+https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
+}