msigdb.genesets: MSigDB Gene Sets

In mw201608/msigdb: MSigDB Gene Set Collections

Description

This function returns pre-compiled MSigDB gene set collections

Usage

msigdb.genesets(sets = NULL, type = c('symbols', 'entrez'), species=c('human', 'mouse'), return.data.frame = FALSE)

Arguments

sets	A vector of possible gene set collections. See details.
type	Type of gene name. Must be one of 'symbols' and 'entrez'.
species	Specifying the species of gene set. Mouse gene sets were converted from human gene sets by orthology mapping.
return.data.frame	See Value.

Details

To view the collections of available MSigDB gene sets, see exported variable msigdb.collections. If sets is NULL, all the collections will be returned.

Value

If return.data.frame is TRUE, returns a data.frame with genes in the first column and set collection names in the second column; otherwise a list with three components:

genesets	List of gene names in each gene set.
geneset.names	Vector of gene set identities. The gene set identities will be in a format of xxx:yyy, where xxx is collection and yyy is gene set name.
geneset.descriptions	Vector of gene set descriptions.

See Also

read.gmt, msigdb.version, msigdb.collections

Examples

#To load human gene ontology gene sets
Result = msigdb.genesets(c('c5.go.bp', 'c5.go.cc', 'c5.go.mf'))

mw201608/msigdb documentation built on Aug. 13, 2021, 10:42 p.m.