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

Andrew Robbins

getProportionMito function

<dl><dt>object</dt>
<dd><code>liger</code> object.</dd>
<dt>use.norm</dt>
<dd>Deprecated Whether to use cell normalized data in
calculating contribution. Default <code>FALSE</code>.</dd>
<dt>pattern</dt>
<dd>Regex pattern for identifying mitochondrial genes. Default
<code>"^mt-"</code> for mouse.</dd></dl>

Arguments

Calculate proportion mitochondrial contribution — getProportionMito

<dl>

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


<dt>use.norm</dt>
<dd>Deprecated Whether to use cell normalized data in
calculating contribution. Default <code>FALSE</code>.</dd>


<dt>pattern</dt>
<dd>Regex pattern for identifying mitochondrial genes. Default
<code>"^mt-"</code> for mouse.</dd>

</dl>

Calculate proportion mitochondrial contribution

getProportionMito: Calculate proportion mitochondrial contribution

Description

Usage

Value

Arguments

Examples