importGeneSetsFromCollection: Imports gene sets from a GeneSetCollection object

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Imports gene sets from a GeneSetCollection object

Description

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.

Usage

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

Arguments

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".
noMatchError	Boolean. Show an error if a collection does not have any matching features. Default TRUE.

Details

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.

Value

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

Author(s)

Joshua D. Campbell

See Also

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

Examples

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

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.