fitBackVar

This funtion fits a second order polynomial to the variance-mean dependence across all genes in log space.

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

fitBackVar function

<dl><dt>x</dt>
<dd>Matrix of transcript counts with genes as rows and cells as columns.</dd>
<dt>mthr</dt>
<dd>Real number. Threshold of log2 mean expression. Genes with mean expression <code>&lt; mthr</code> are discarded prior to fitting the polynomial. Default is -1.</dd></dl>

Arguments

Function for computing a background model of gene expression variability — fitBackVar

<dl>

<dt>x</dt>
<dd>Matrix of transcript counts with genes as rows and cells as columns.</dd>


<dt>mthr</dt>
<dd>Real number. Threshold of log2 mean expression. Genes with mean expression <code>&lt; mthr</code> are discarded prior to fitting the polynomial. Default is -1.</dd>

</dl>

fitBackVar: Function for computing a background model of gene expression variability

Description

Usage

Value

Arguments

Examples