% 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

}