Fetch MSigDB gene sets by pathway name — getGeneSets • geneSetSimplifyR

Fetches gene-set memberships from MSigDB via msigdbr::msigdbr() and returns them in the named-list format expected by geneSetSimplifyR() (pathway name -> character vector of gene IDs).

Useful in two situations:

Inspecting the gene members of specific pathways (e.g. the top pathways from a cluster after running the workflow).
Building a geneSetsList from scratch without going through pairedGSEA::prepare_msigdb().

Usage

getGeneSets(
  pathway_names = NULL,
  species = "Homo sapiens",
  collection = "C5",
  subcollection = NULL,
  gene_id_type = c("ensembl_gene", "gene_symbol", "entrez_gene")
)

Arguments

pathway_names: Character vector of MSigDB pathway names (i.e. gs_name values). If NULL (default), all pathways in the requested collection/subcollection are returned.
species: Species, passed to msigdbr::msigdbr(). Default "Homo sapiens".
collection: MSigDB collection (e.g. "C5", "H", "C2"). Default "C5".
subcollection: Optional MSigDB sub-collection (e.g. "GO:BP"). NULL (default) returns the full collection.
gene_id_type: Which gene identifier to use for the returned vectors. One of "ensembl_gene" (default), "gene_symbol", or "entrez_gene".

Value

A named list where each element is a character vector of gene IDs for a pathway. Names are pathway names (gs_name).

Examples

# \donttest{
if (requireNamespace("msigdbr", quietly = TRUE)) {
  # Hallmark gene sets (gene symbols)
  hallmark <- getGeneSets(collection = "H", gene_id_type = "gene_symbol")

  # Just the genes of two specific pathways
  twoSets <- getGeneSets(
    pathway_names = c("HALLMARK_APOPTOSIS", "HALLMARK_HYPOXIA"),
    collection = "H",
    gene_id_type = "gene_symbol"
  )
  lengths(twoSets)
}
#> Downloading gene sets (first use only, may take a few minutes)...
#> HALLMARK_APOPTOSIS   HALLMARK_HYPOXIA 
#>                161                200 
# }