importMitoGeneSet {singleCellTK} | R Documentation

## Import mitochondrial gene sets

### Description

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.

### Usage

    importMitoGeneSet(inSCE, reference, id, by, collectionName)

### Arguments

`inSCE` | Input SingleCellExperiment object.
`reference` | Character. Species available are "human" and "mouse".
`id` | Types of gene id. Now it supports "symbol", "entrez", "ensemble" and "ensemble_transcriptID".
`by` | Character. Describes the location within `inSCE` where the gene identifiers in the mitochondrial gene sets 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`. See featureIndex for more information. Default `"rownames"`.
`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.

### Details

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.

### Value

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

### Author(s)

Rui Hong

### See Also

importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, and GeneSetCollection objects.

### Examples

    data(scExample)
    sce <- importMitoGeneSet(inSCE = sce,
                             reference = "human",
                             id = "ensemble",
                             collectionName = "human_mito",
                             by = "rownames")

[Package singleCellTK version 2.2.0 Index]