R/importGeneSets.R
importGeneSetsFromCollection.Rd
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 |
by | Character, character vector, or NULL. 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 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.
importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, and importGeneSetsFromMSigDB for importing MSigDB gene sets.
Joshua D. Campbell
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