row_gmean

A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.

Saket Choudhary

sctransform

Variance Stabilizing Transformations for Single Cell UMI Data

Christoph Hafemeister

Rahul Satija

row_gmean function

<dl><dt>x</dt>
<dd>matrix of class <code>matrix</code> or <code>dgCMatrix</code></dd>
<dt>eps</dt>
<dd>small value to add to x to avoid log(0); default is 1</dd></dl>

Arguments

Geometric mean per row — row_gmean

<dl>

<dt>x</dt>
<dd>matrix of class <code>matrix</code> or <code>dgCMatrix</code></dd>


<dt>eps</dt>
<dd>small value to add to x to avoid log(0); default is 1</dd>

</dl>

row_gmean: Geometric mean per row

Description

Usage

Value

Arguments