importMitoGeneSet: Import mitochondrial gene sets

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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 = "human",
  id = "ensembl",
  by = "rownames",
  collectionName = "mito",
  noMatchError = TRUE
)

Arguments

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

Details

The gene identifiers of mitochondrial genes will be loaded with "data(AllMito)". Currently, it supports human and mouse references. 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 = "ensembl",
                         collectionName = "human_mito",
                         by = "rownames")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.