importGeneSetsFromCollection: Imports gene sets from a GeneSetCollection object
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Details Value Author(s) See Also Examples

Converts a list of gene sets stored in a GeneSetCollection object and stores it in the metadata of the SingleCellExperiment object. These gene sets can be used in downstream quality control and analysis functions in singleCellTK.

importGeneSetsFromCollection(
  inSCE,
  geneSetCollection,
  collectionName = "GeneSetCollection",
  by = "rownames"
)

`inSCE`	Input SingleCellExperiment object.
`geneSetCollection`	A GeneSetCollection object. See GeneSetCollection for more details.
`collectionName`	Character. Name of collection to add gene sets to. If this collection already exists in `inSCE`, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default `GeneSetCollection`.
`by`	Character, character vector, or NULL. Describes the location within `inSCE` where the gene identifiers in `geneSetCollection` should be mapped. If set to `"rownames"` then the features will be searched for among `rownames(inSCE)`. This can also be set to one of the column names of `rowData(inSCE)` in which case the gene identifies will be mapped to that column in the `rowData` of `inSCE`. `by` can be a vector the same length as the number of gene sets in the `GeneSetCollection` and the elements of the vector can point to different locations within `inSCE`. Finally, `by` can be `NULL`. In this case, the location of the gene identifiers in `inSCE` should be saved in the description slot for each gene set in the `GeneSetCollection`. See featureIndex for more information. Default `"rownames"`.

The gene identifiers in gene sets in the GeneSetCollection will be mapped to the rownames of inSCE using the by parameter and stored in a GeneSetCollection object from package GSEABase. This object is stored in metadata(inSCE)$sctk$genesets, which can be accessed in downstream analysis functions such as runCellQC.

A SingleCellExperiment object with gene set from collectionName output stored to the metadata slot.

Joshua D. Campbell

importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, and importGeneSetsFromMSigDB for importing MSigDB gene sets.

data(scExample)
library(GSEABase)
gs1 <- GeneSet(setName = "geneset1", geneIds = rownames(sce)[1:10])
gs2 <- GeneSet(setName = "geneset2", geneIds = rownames(sce)[11:20])
gsc <- GeneSetCollection(list(gs1, gs2))
sce <- importGeneSetsFromCollection(inSCE = sce,
                                    geneSetCollection = gsc,
                                    by = "rownames")