getProportionMito: Calculate proportion mitochondrial contribution

In rliger: Linked Inference of Genomic Experimental Relationships

Calculate proportion mitochondrial contribution

Description

Calculates proportion of mitochondrial contribution based on raw or normalized data.

Usage

getProportionMito(object, use.norm = FALSE, pattern = "^mt-")

Arguments

object	liger object.
use.norm	Deprecated Whether to use cell normalized data in calculating contribution. Default FALSE.
pattern	Regex pattern for identifying mitochondrial genes. Default "^mt-" for mouse.

Value

Named vector containing proportion of mitochondrial contribution for each cell.

Note

getProportionMito will be deprecated because runGeneralQC generally covers and expands its use case.

Examples

# Example dataset does not contain MT genes, expected to see a message
pbmc$mito <- getProportionMito(pbmc)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.