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Gene set enrichment via MSigDB

Source: R/enrich_msigdb.R
enrich_msigdb.Rd

Enrichment analysis against MSigDB gene sets via hypergeometric test. Supports MSigDB categories, subcategories, and specified gene sets. Requires the msigdbr package.

Use cases:

  • Drug perturbations: category = "C2", subcategory = "CGP" (chemical and genetic perturbations)

  • TF targets: category = "C3", subcategory = "TFT:GTRD"

  • Hallmarks: category = "H", subcategory = NULL (no subcategory)

  • GO: category = "C5", subcategory = "BP" (GO biological process)

Multiple testing: P-values are adjusted (Benjamini-Hochberg) per module across the gene-set tests within that module.

Usage

enrich_msigdb(
  gene_list,
  universe,
  category = NULL,
  subcategory = NULL,
  gene_sets = NULL,
  species = "Homo sapiens",
  db_species = "HS",
  name = NULL,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  minGSSize = 10,
  maxGSSize = 500
)

Arguments

gene_list

A named list of gene vectors, or a data.frame with Feature and Module columns from WGCNA_module().

universe

Background genes (required).

category

MSigDB category (default: NULL). See msigdbr::msigdbr_collections(db_species = "HS"/"MM") for available options. Not required when gene_sets is provided; in that case all collections are searched to locate the named gene sets.

subcategory

MSigDB subcategory (default: NULL). Set to NULL to include all subcategories of category.

gene_sets

Optional character vector of specific MSigDB gene set names to include (e.g., c("HALLMARK_APOPTOSIS", "HALLMARK_P53_PATHWAY")). When provided, msigdbr is queried across all collections to find these gene sets, so category and subcategory are not required. If NULL (default), all gene sets in the category/subcategory are used.

species

Species of input genes (default: "Homo sapiens"). See msigdbr::msigdbr_species() for available options.

db_species

Species of MSigDB genesets (default: "HS"). Use "MM" for mouse-native gene sets. If species and db_species mismatch, db_species MSigDB will be used with ortholog mapping to species.

name

Name for the output list element. If NULL, auto-derived from category (e.g., "C2" names the output element "C2"). If category is also NULL, it uses "msigdb".

pvalueCutoff

Adjusted p-value cutoff (default: 0.05).

pAdjustMethod

P-value adjustment method (default: "BH").

minGSSize

Minimum gene set size (default: 10).

maxGSSize

Maximum gene set size (default: 500).

Value

A named list with one element: a data.frame with columns Cluster, ID, Description, GeneRatio, BgRatio, pvalue, p.adjust, Count, geneID.

Examples

if (requireNamespace("msigdbr", quietly = TRUE)) {
    data(example_net)
    example_module <- WGCNA_module(example_net) |>
        dplyr::filter(Module %in% c("1", "2"))
    hallmark_msigdb <- enrich_msigdb(example_module, category = "MH",
        species = "Mus musculus", db_species = "MM",
        minGSSize = 1,
        pvalueCutoff = 0.9,
        universe = WGCNA_module(example_net, exclude_grey = FALSE)$Feature)
}
#> Processing gene list: 1
#> Processing gene list: 2