GetMsigdbGeneSet: GetMsigdbGeneSet

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

GetMsigdbGeneSet

Description

a slightly extended escape::getGeneSet wrapper to deal with one-step gene set parsing, which can't parse hierarchical gene sets (C5 + GO:BP) and non-hierarchical gene sets (hallmark, C2 itself, etc) at the same time.

Usage

GetMsigdbGeneSet(msigdbGeneSets = "H")

Arguments

msigdbGeneSets

a character vector of gene sets that is either a top level msigdb gene set name (e.g. "H" for hallmark or "C2" for curated gene sets), or a common hierarchical gene set in a large top level (e.g. C5;BP for GO:BP annotations.)

Value

a named list of gene sets fetched by msigdbr.

bimberlabinternal/CellMembrane documentation built on Nov. 15, 2024, 9:34 p.m.