plotExpNoise

Plotting noise (epsilon) as a function of normalized or non-normalized expression for a given gene.

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

plotExpNoise function

<dl><dt>g</dt>
<dd>Valid gene ID with available expression and noise estimates.</dd>
<dt>object</dt>
<dd>RaceID <code>SCseq</code> object.</dd>
<dt>noise</dt>
<dd>List object returned by the <code>compTBNoise</code> function.</dd>
<dt>set</dt>
<dd>Set of valid cluster numbers. Default is <code>NULL</code> and data are plotted for cells from all clusters.</dd>
<dt>ps</dt>
<dd>Real number. Pseudo-count added to noise and expression estimates. Default is 0.1.</dd>
<dt>norm</dt>
<dd>logical. If <code>FALSE</code>, then noise is plotted versus non-normalized expression. Default is <code>TRUE</code> and noise is plotted against normalized expression.</dd>
<dt>...</dt>
<dd>Additional arguments of <code>plot</code> function.</dd></dl>

Arguments

Noise-expression scatter plot — plotExpNoise

<dl>

<dt>g</dt>
<dd>Valid gene ID with available expression and noise estimates.</dd>


<dt>object</dt>
<dd>RaceID <code>SCseq</code> object.</dd>


<dt>noise</dt>
<dd>List object returned by the <code>compTBNoise</code> function.</dd>


<dt>set</dt>
<dd>Set of valid cluster numbers. Default is <code>NULL</code> and data are plotted for cells from all clusters.</dd>


<dt>ps</dt>
<dd>Real number. Pseudo-count added to noise and expression estimates. Default is 0.1.</dd>


<dt>norm</dt>
<dd>logical. If <code>FALSE</code>, then noise is plotted versus non-normalized expression. Default is <code>TRUE</code> and noise is plotted against normalized expression.</dd>


<dt>...</dt>
<dd>Additional arguments of <code>plot</code> function.</dd>

</dl>

plotExpNoise: Noise-expression scatter plot

Description

Usage

Value

Arguments