DESeq2_analyze: Differential Gene Expression Analysis using 'DESeq2'

In TransProR: Analysis and Visualization of Multi-Omics Data

Differential Gene Expression Analysis using 'DESeq2'

Description

'DESeq2': Differential gene expression analysis based on the negative binomial distribution. This function utilizes the 'DESeq2' package to conduct differential gene expression analysis. It processes tumor and normal expression data, applies DESeq2 analysis, and outputs the results along with information on gene expression changes.

Usage

DESeq2_analyze(
  tumor_file,
  normal_file,
  output_file,
  logFC = 2.5,
  p_value = 0.01
)

Arguments

tumor_file	Path to the tumor data file (RDS format).
normal_file	Path to the normal data file (RDS format).
output_file	Path to save the output DEG data (RDS format).
logFC	Threshold for log fold change.
p_value	Threshold for p-value.

Details

The DESeq2 methodology is based on modeling count data using a negative binomial distribution, which allows for handling the variability observed in gene expression data, especially in small sample sizes. This approach is well-suited for RNA-Seq data analysis.

Value

A data frame of differential expression results.

References

DESeq2:Differential gene expression analysis based on the negative binomial distribution. For more information, visit the page: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/

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_DESeq2.rds")

DEG_DESeq2 <- DESeq2_analyze(
  tumor_file = tumor_file,
  normal_file = normal_file,
  output_file = output_file,
  2.5,
  0.01
)

# View the top 5 rows of the result
head(DEG_DESeq2, 5)

TransProR documentation built on April 4, 2025, 3:16 a.m.