sctkListGeneSetCollections {singleCellTK} | R Documentation

## Lists imported GeneSetCollections

### Description

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

### Usage

    sctkListGeneSetCollections(inSCE)

### 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

    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)

[Package singleCellTK version 2.2.0 Index]