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)
#> Warning: `getProportionMito()` was deprecated in rliger 1.99.0.
#> ℹ Please use `runGeneralQC()` instead.
#> ! Zero proportion detected in all cells