Lists imported GeneSetCollections

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

sctkListGeneSetCollections(inSCE)

Arguments

inSCE

A SingleCellExperiment object.

Value

Character vector.

See also

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

Author

Joshua D. Campbell

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)