Returns a vector of GeneSetCollections that have been
imported and stored in metadata(inSCE)$sctk$genesets
.
sctkListGeneSetCollections(inSCE)
A SingleCellExperiment object.
Character vector.
importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, GeneSetCollection objects, and importGeneSetsFromMSigDB for importing MSigDB gene sets.
data(scExample)
library(GSEABase)
gs1 <- GeneSet(setName = "geneset1", geneIds = rownames(sce)[seq(10)])
gs2 <- GeneSet(setName = "geneset2", geneIds = rownames(sce)[seq(11,20)])
gsc1 <- GeneSetCollection(gs1)
gsc2 <- 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)