% 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.

}