sig_gsea: Perform Gene Set Enrichment Analysis (GSEA)

In IOBR: Immune Oncology Biological Research

Perform Gene Set Enrichment Analysis (GSEA)

Description

Conducts Gene Set Enrichment Analysis to identify significantly enriched gene sets from differential gene expression data. Supports MSigDB gene sets or custom gene signatures, and generates comprehensive visualizations and statistical results.

Usage

sig_gsea(
  deg,
  genesets = NULL,
  path = NULL,
  gene_symbol = "symbol",
  logfc = "log2FoldChange",
  org = c("hsa", "mus"),
  msigdb = TRUE,
  category = "H",
  subcategory = NULL,
  palette_bar = "jama",
  palette_gsea = 2,
  cols_gsea = NULL,
  cols_bar = NULL,
  show_bar = 10,
  show_col = FALSE,
  show_plot = FALSE,
  show_gsea = 8,
  show_path_n = 20,
  plot_single_sig = FALSE,
  project = "custom_sig",
  minGSSize = 10,
  maxGSSize = 500,
  verbose = TRUE,
  seed = FALSE,
  fig.type = "pdf",
  print_bar = TRUE
)

Arguments

deg	Data frame containing differential expression results with gene symbols and log fold changes.
genesets	List of custom gene sets for enrichment analysis. If 'NULL', MSigDB gene sets are used based on 'org' and 'category'. Default is 'NULL'.
path	Character string specifying the directory path for saving results. Default is 'NULL'.
gene_symbol	Character string specifying the column name in 'deg' containing gene symbols. Default is '"symbol"'.
logfc	Character string specifying the column name in 'deg' containing log fold change values. Default is '"log2FoldChange"'.
org	Character string specifying the organism. Options are '"hsa"' (Homo sapiens) or '"mus"' (Mus musculus). Default is '"hsa"'.
msigdb	Logical indicating whether to use MSigDB gene sets. Default is 'TRUE'.
category	Character string specifying the MSigDB category (e.g., '"H"' for Hallmark, '"C2"' for curated gene sets). Default is '"H"'.
subcategory	Character string specifying the MSigDB subcategory to filter gene sets. Default is 'NULL'.
palette_bar	Character string or integer specifying the color palette for bar plots. Default is '"jama"'.
palette_gsea	Integer specifying the color palette for GSEA plots. Default is '2'.
cols_gsea	Character vector specifying custom colors for GSEA enrichment plots. If 'NULL', colors are automatically generated. Default is 'NULL'.
cols_bar	Character vector specifying custom colors for the enrichment bar plot. If 'NULL', colors are automatically generated. Default is 'NULL'.
show_bar	Integer specifying the number of top enriched gene sets to display in the bar plot. Default is '10'.
show_col	Logical indicating whether to display color names in the bar plot. Default is 'FALSE'.
show_plot	Logical indicating whether to display GSEA enrichment plots. Default is 'FALSE'.
show_gsea	Integer specifying the number of top significant gene sets for which to generate GSEA plots. Default is '8'.
show_path_n	Integer specifying the number of pathways to display in GSEA plots. Default is '20'.
plot_single_sig	Logical indicating whether to generate separate plots for each significant gene set. Default is 'TRUE'.
project	Character string specifying the project name for output files. Default is '"custom_sig"'.
minGSSize	Integer specifying the minimum gene set size for analysis. Default is '10'.
maxGSSize	Integer specifying the maximum gene set size for analysis. Default is '500'.
verbose	Logical indicating whether to display progress messages. Default is 'TRUE'.
seed	Logical indicating whether to set a random seed for reproducibility. Default is 'FALSE'.
fig.type	Character string specifying the file format for saving plots (e.g., '"pdf"', '"png"'). Default is '"pdf"'.
print_bar	Logical indicating whether to save and print the bar plot. Default is 'TRUE'.

Value

List containing:

up

Data frame of up-regulated enriched gene sets

down

Data frame of down-regulated enriched gene sets

all

Complete GSEA results

plot_top

GSEA enrichment plot for top gene sets

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
genes <- c(
  "TP53", "BRCA1", "EGFR", "MYC", "KRAS", "PTEN", "APC", "RB1",
  "CDKN2A", "VHL", "ATM", "ATR", "CHEK2", "PALB2", "RAD51", "MDM2",
  "CDK4", "CDK6", "CCND1", "CCNE1", "CDK2", "E2F1", "E2F2", "E2F3",
  "ARF1", "ARF3", "ARF4", "ARF5", "ARF6", "GSK3B", "AKT1", "AKT2",
  "PIK3CA", "PIK3CB", "PIK3CD", "PIK3CG", "PIK3R1", "PIK3R2", "PIK3R3"
)
deg <- data.frame(
  symbol = genes,
  log2FoldChange = rnorm(length(genes), mean = 0, sd = 2),
  padj = runif(length(genes), 0, 0.1)
)
signature <- list(
  DNA_Repair = c(
    "TP53", "BRCA1", "ATM",
    "ATR", "CHEK2", "PALB2", "RAD51"
  ),
  Cell_Cycle = c(
    "TP53", "MYC",
    "RB1", "CDKN2A", "CDK4",
    "CDK6", "CCND1", "CCNE1",
    "CDK2", "E2F1", "E2F2", "E2F3"
  ),
  PI3K_AKT = c(
    "AKT1", "AKT2",
    "PIK3CA", "PIK3CB", "PIK3CD",
    "PIK3CG", "PIK3R1", "PIK3R2", "PIK3R3"
  )
)

res <- sig_gsea(
  deg = deg,
  genesets = signature,
  path = tempdir(),
  show_plot = FALSE,
  print_bar = FALSE
)
print(names(res))

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