Description Usage Arguments Value Author(s) See Also Examples
View source: R/importGeneSets.R
Returns a vector of GeneSetCollections that have been
imported and stored in metadata(inSCE)$sctk$genesets
.
1 | sctkListGeneSetCollections(inSCE)
|
inSCE |
A SingleCellExperiment object. |
Character vector.
Joshua D. Campbell
importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, GeneSetCollection objects, and importGeneSetsFromMSigDB for importing MSigDB gene sets.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(scExample)
library(GSEABase)
gs1 <- GeneSet(setName = "geneset1", geneIds = rownames(sce)[1:10])
gs2 <- GeneSet(setName = "geneset2", geneIds = rownames(sce)[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)
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