getProportionMito {rliger}

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)