merge_gs: Merge Selected Major GeneSets from MsigDB

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Merge Selected Major GeneSets from MsigDB

Description

merge_gs combines selected major gene set collections (e.g. "H", "C1" ) together, and return a list object with sub-collections as elements. Each element contains a vector of genes belong to that sub-collection gene set.

Usage

merge_gs(
  all_gs2gene = all_gs2gene,
  use_gs = c("H", "CP:BIOCARTA", "CP:REACTOME", "CP:KEGG", "C5")
)

Arguments

all_gs2gene	list, the list returned by gs.preload().
use_gs	a vector of characters, names of major gene set collections. Users can call all_gs2gene_info to see all the available collections. Default is c("H", "CP:BIOCARTA", "CP:REACTOME", "CP:KEGG").

Value

Return a list object with sub-collection gene sets as elements. Each element contains a vector of genes.

Examples

gs.preload(use_spe='Homo sapiens',update=FALSE)
use_gs2gene <- merge_gs(all_gs2gene=all_gs2gene,
                       use_gs=c('H','CP:BIOCARTA','CP:REACTOME','CP:KEGG','C5'))

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.