Extract a collection of gene sets from the MSigDB object — get_genesets • DIANNmv

Extract a collection of gene sets from the MSigDB object

Usage

get_genesets(
  db,
  collection = c("c2", "c5", "h"),
  subcollection = c("GOBP", "GOCC", "GOMF", "KEGG")
)

Arguments

db: An MSigDB object downloaded with load_msigdb()
collection: Specifies which collection of gene sets to use. Options are: c2 (e.g. Reactome, KEGG), c5 (GO sets), or h (cancer hallmarks)
subcollection: Specifies which subcollection to use. E.g. 'Reactome' or 'KEGG' for c2, or 'GOBP/GOCC/GOMF' for 'c5'

Value

A list with gene sets

Examples

if (FALSE) { # \dontrun{
Reactome <- get_genesets(db, collection = 'c2', subcollection = 'Reactome')
} # }