sctkListGeneSetCollections: Lists imported GeneSetCollections

Description Usage Arguments Value Author(s) See Also Examples

View source: R/importGeneSets.R

Description

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

Usage

1

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

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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)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.