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