iobr_deg: Differential Expression Analysis

In IOBR: Immune Oncology Biological Research

Differential Expression Analysis

Description

Performs differential expression analysis on gene expression data using either DESeq2 or limma. Includes pre-processing steps like filtering low count data, and calculates fold changes and adjusted p-values. Optionally generates volcano plots and heatmaps.

Usage

iobr_deg(
  eset,
  annotation = NULL,
  id_anno = NULL,
  pdata,
  group_id = "group",
  pdata_id = "ID",
  array = FALSE,
  method = c("DESeq2", "limma"),
  contrast = c("High", "Low"),
  path = NULL,
  padj_cutoff = 0.01,
  logfc_cutoff = 0.5,
  volcano_plot = FALSE,
  col_volcano = 1,
  heatmap = TRUE,
  col_heatmap = 1,
  parallel = FALSE
)

Arguments

eset	A matrix of gene expression data where rows represent genes and columns represent samples.
annotation	Optional data frame for mapping gene IDs to gene names. Default is 'NULL'.
id_anno	Character string specifying the identifier column in annotation. Default is 'NULL'.
pdata	A data frame containing sample information and grouping labels.
group_id	Character string specifying the column name in 'pdata' containing grouping labels. Default is '"group"'.
pdata_id	Character string specifying the column name in 'pdata' for sample IDs. Default is '"ID"'.
array	Logical indicating whether to perform quantile normalization. Default is 'FALSE'.
method	Character string specifying the method: '"DESeq2"' or '"limma"'. Default is '"DESeq2"'.
contrast	Character vector of length 2 specifying contrast groups. Default is 'c("High", "Low")'.
path	Character string for output directory. Default is 'NULL'.
padj_cutoff	Numeric cutoff for adjusted p-values. Default is '0.01'.
logfc_cutoff	Numeric log2 fold change cutoff. Default is '0.5'.
volcano_plot	Logical indicating whether to generate a volcano plot. Default is 'FALSE'.
col_volcano	Integer specifying color index for volcano plot. Default is '1'.
heatmap	Logical indicating whether to generate a heatmap. Default is 'TRUE'.
col_heatmap	Integer specifying color index for heatmap. Default is '1'.
parallel	Logical indicating whether to run in parallel. Default is 'FALSE'.

Value

Data frame containing differentially expressed genes with statistics including log2 fold changes and adjusted p-values.

Author(s)

Dongqiang Zeng

Examples

# Simulate data
set.seed(123)
sim_eset <- matrix(abs(rnorm(100 * 20)), 100, 20)
rownames(sim_eset) <- paste0("Gene", 1:100)
colnames(sim_eset) <- paste0("Sample", 1:20)

sim_pdata <- data.frame(
  ID = paste0("Sample", 1:20),
  group = rep(c("High", "Low"), each = 10)
)

# Run DEG analysis
deg <- iobr_deg(
  eset = sim_eset, pdata = sim_pdata,
  group_id = "group", pdata_id = "ID",
  method = "limma", contrast = c("High", "Low"),
  heatmap = FALSE
)
if (!is.null(deg)) head(deg)

IOBR documentation built on May 30, 2026, 5:07 p.m.