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" )
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 |
by | Character or character vector. Describes the
location within |
A SingleCellExperiment object
with gene set from collectionName
output stored to the
metadata slot.
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.
importGeneSetsFromCollection for importing from GeneSetCollection objects, importGeneSetsFromGMT for importing from GMT files, and importGeneSetsFromMSigDB for importing MSigDB gene sets.
Joshua D. Campbell
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")