getProportionMito

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

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

getProportionMito function

<dl><dt>object</dt>
<dd><code>liger</code> object.</dd>
<dt>use.norm</dt>
<dd>Whether to use cell normalized data in calculating contribution (default FALSE).</dd>
<dt>mito.pattern</dt>
<dd>Regex pattern for identifying mitochondrial genes. Default "^mt-" typically goes for mouse.
May use "^MT-" for human.</dd></dl>

Arguments

Calculate proportion mitochondrial contribution — getProportionMito

<dl>

<dt>object</dt>
<dd><code>liger</code> object.</dd>


<dt>use.norm</dt>
<dd>Whether to use cell normalized data in calculating contribution (default FALSE).</dd>


<dt>mito.pattern</dt>
<dd>Regex pattern for identifying mitochondrial genes. Default "^mt-" typically goes for mouse.
May use "^MT-" for human.</dd>

</dl>

Calculate proportion mitochondrial contribution

getProportionMito: Calculate proportion mitochondrial contribution

Description

Usage

Value

Arguments

Examples