iobr_deg: iobr_deg

In IOBR/IOBR: Immune Oncology Biological Research

iobr_deg

Description

This function performs differential expression analysis on gene expression data using the DESeq2 or limma method. It filters low count data, calculates fold changes and adjusted p-values, and identifies differentially expressed genes (DEGs) based on specified cutoffs. It also provides optional visualization tools such as volcano plots and heatmaps. The function saves the results as an RData file and an Excel file.

Usage

iobr_deg(
  eset,
  annotation = NULL,
  id_anno = NULL,
  pdata,
  group_id = "group",
  pdata_id = "ID",
  array = FALSE,
  method = "DESeq2",
  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	The gene expression data matrix
annotation	(Optional) The annotation object for mapping gene IDs to gene names. Default is NULL.
id_anno	Identifier of annotation data matched to row names of eset
pdata	The DataFrame containing sample information and group labels.
group_id	The column name in "pdata" that specifies the group labels. Default value is "group".
pdata_id	The column name in "pdata" that specifies the sample IDs. Default value is "ID".
array	Logical value indicating whether to normalize the gene expression data using quantile normalization. Default value is TRUE.
method	The method to be used for differential expression analysis. Options are "DESeq2" or "limma". Default value is "DESeq2".
contrast	A character vector specifying the contrast for the analysis. The first and second elements are the names of the two groups being compared. Default value is "High" and "Low".
path	path to save results
padj_cutoff	The adjusted p-value cutoff for determining significance. Default value is 0.01.
logfc_cutoff	The log2 fold change cutoff for determining significance. Default value is 0.5.
volcano_plot	Logical value indicating whether to generate a volcano plot. Default value is FALSE.
col_volcano	The color index for plotting the volcano plot. Default value is 1.
heatmap	Logical value indicating whether to generate a heatmap. Default value is TRUE.
col_heatmap	The color index for plotting the heatmap. Default value is 1.
parallel	default is FALSE

Value

DEG object

Author(s)

Dongqiang Zeng

Examples

data("eset_stad", package = "IOBR")
data("stad_group", package = "IOBR")
library(DESeq2)
deg<- iobr_deg(eset  = eset_stad, pdata = stad_group, group_id = "subtype", pdata_id = "ID", array = FALSE, method = "DESeq2", contrast = c("EBV","GS"), path = "STAD")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.