Imports gene sets from a list

Converts a list of gene sets into a GeneSetCollection 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.

importGeneSetsFromList(
  inSCE,
  geneSetList,
  collectionName = "GeneSetCollection",
  by = "rownames",
  noMatchError = TRUE
)

Arguments

inSCE

Input SingleCellExperiment object.

geneSetList

Named List. A list containing one or more gene sets. Each element of the list should be a character vector of gene identifiers. The names of the list will be become the gene set names in the GeneSetCollection object.

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 or character vector. Describes the location within inSCE where the gene identifiers in geneSetList 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. Finally, by can be a vector the same length as the number of gene sets in geneSetList and the elements of the vector can point to different locations within inSCE. See featureIndex for more information. Default "rownames".

noMatchError

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

Value

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

Details

The gene identifiers in gene sets in geneSetList 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.

See also

importGeneSetsFromCollection for importing from GeneSetCollection objects, importGeneSetsFromGMT for importing from GMT files, and importGeneSetsFromMSigDB for importing MSigDB gene sets.

Author

Joshua D. Campbell

Examples

data(scExample)

# Generate gene sets from 'rownames'
gs1 <- rownames(sce)[seq(10)]
gs2 <- rownames(sce)[seq(11,20)]
gs <- list("geneset1" = gs1, "geneset2" = gs2)
sce <- importGeneSetsFromList(inSCE = sce,
                              geneSetList = gs,
                              by = "rownames")

# Generate a gene set for mitochondrial genes using
# Gene Symbols stored in 'rowData'
mito.ix <- grep("^MT-", rowData(sce)$feature_name)
mito <- list(mito = rowData(sce)$feature_name[mito.ix])
sce <- importGeneSetsFromList(inSCE = sce,
                             geneSetList = mito,
                             by = "feature_name")