sctkListGeneSetCollections: Lists imported GeneSetCollections

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Lists imported GeneSetCollections

Description

Returns a vector of GeneSetCollections that have been imported and stored in metadata(inSCE)$sctk$genesets.

Usage

sctkListGeneSetCollections(inSCE)

Arguments

inSCE

A SingleCellExperiment object.

Value

Character vector.

Author(s)

Joshua D. Campbell

See Also

importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, GeneSetCollection objects, and importGeneSetsFromMSigDB for importing MSigDB gene sets.

Examples

data(scExample)
gs1 <- GSEABase::GeneSet(setName = "geneset1",
                         geneIds = rownames(sce)[seq(10)])
gs2 <- GSEABase::GeneSet(setName = "geneset2",
                         geneIds = rownames(sce)[seq(11,20)])
gsc1 <- GSEABase::GeneSetCollection(gs1)
gsc2 <- GSEABase::GeneSetCollection(gs2)
sce <- importGeneSetsFromCollection(inSCE = sce,
                                    geneSetCollection = gsc1,
                                    by = "rownames",
                                    collectionName = "Collection1")
sce <- importGeneSetsFromCollection(inSCE = sce,
                                    geneSetCollection = gsc2,
                                    by = "rownames",
                                    collectionName = "Collection2")
collections <- sctkListGeneSetCollections(sce)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.