--- a
+++ b/man/Wilcoxon_analyze.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/WilcoxonAnalyze.R
+\name{Wilcoxon_analyze}
+\alias{Wilcoxon_analyze}
+\title{Differential Gene Expression Analysis Using Wilcoxon Rank-Sum Test}
+\usage{
+Wilcoxon_analyze(
+  tumor_file,
+  normal_file,
+  output_file,
+  logFC_threshold = 2.5,
+  fdr_threshold = 0.05
+)
+}
+\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{fdr_threshold}{Threshold for FDR for filtering significant genes.}
+}
+\value{
+A data frame of differential expression results.
+}
+\description{
+This function performs differential gene expression analysis using Wilcoxon rank-sum tests.
+It reads tumor and normal expression data, performs TMM normalization using 'edgeR', and uses Wilcoxon rank-sum tests to identify differentially expressed genes.
+}
+\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(), "Wilcoxon_rank_sum_testoutRst.rds")
+
+# Run the Wilcoxon rank sum test
+outRst <- Wilcoxon_analyze(
+  tumor_file = tumor_file,
+  normal_file = normal_file,
+  output_file = output_file,
+  logFC_threshold = 2.5,
+  fdr_threshold = 0.01
+)
+
+# View the top 5 rows of the result
+head(outRst, 5)
+}
+\references{
+Li, Y., Ge, X., Peng, F., Li, W., & Li, J. J. (2022). Exaggerated False Positives by Popular
+Differential Expression Methods When Analyzing Human Population Samples. Genome Biology, 23(1), 79.
+DOI: https://doi.org/10.1186/s13059-022-02648-4.
+}