Imports mitochondrial gene sets 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.
importMitoGeneSet(inSCE, reference, id, by, collectionName)
inSCE | Input SingleCellExperiment object. |
---|---|
reference | Character. Species available are "human" and "mouse". |
id | Types of gene id. Now it supports "symbol", "entrez", "ensembl" and "ensemblTranscriptID". |
by | Character. Describes the location within |
collectionName | Character. Name of collection to add gene sets to.
If this collection already exists in |
A SingleCellExperiment object
with gene set from collectionName
output stored to the
metadata slot.
The gene identifiers of mitochondrial genes will be loaded with
"data(AllMito)". Currently, it supports human and mouse reference.
Also, it supports entrez ID, gene symbol, ensemble ID and ensemble transcript ID.
They will be mapped to the IDs in 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 GeneSetCollection objects.
Rui Hong
data(scExample) sce <- importMitoGeneSet(inSCE = sce, reference = "human", id = "ensembl", collectionName = "human_mito", by = "rownames")