get_nz_median2

Get median of non zero UMIs from a count matrix

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

get_nz_median2 function

<dl><dt>umi</dt>
<dd>Count matrix</dd>
<dt>genes</dt>
<dd>A vector of genes to consider for calculating
the median. Default is NULL which uses all genes.</dd></dl>

Arguments

Get median of non zero UMIs from a count matrix — get_nz_median2

<dl>

<dt>umi</dt>
<dd>Count matrix</dd>


<dt>genes</dt>
<dd>A vector of genes to consider for calculating
the median. Default is NULL which uses all genes.</dd>

</dl>

get_nz_median2: Get median of non zero UMIs from a count matrix

Description

Usage

Value

Arguments