plotRegNB

This function plots the parameters obatined by the negative binomial regression of the transcript counts on the total transcript count in each cells.
Smoothed parameter estimates are also shown.

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

plotRegNB function

<dl><dt>expData</dt>
<dd>Matrix of gene expression values with genes as rows and cells as columns. The matrix needs to contain the same cell IDs as columns like the input matrix.
used to derive the pruned k nearest neighbours with the <code>pruneKnn</code> function.</dd>
<dt>y</dt>
<dd>List object returned by the <code>compNoise</code> or <code>pruneKnn</code> function (if run with <code>regNB=TRUE</code>).</dd>
<dt>par.nb</dt>
<dd>Parameter to be plotted, i.e. valid column of <code>res$regData$nbRegr</code>.
of the log total UMI count. <code>intercept</code> is the intercept inferred by the regression. Default is <code>NULL</code> and <code>theta</code> is shown.</dd>
<dt>span</dt>
<dd>Positive real number. Parameter for loess-regression (see <code>large</code>) controlling the degree of smoothing. Default is 0.75.</dd>
<dt>...</dt>
<dd>Additional arguments for <code>plot</code>.</dd></dl>

Arguments

Function for plotting negative binomial regression — plotRegNB

<dl>

<dt>expData</dt>
<dd>Matrix of gene expression values with genes as rows and cells as columns. The matrix needs to contain the same cell IDs as columns like the input matrix.
used to derive the pruned k nearest neighbours with the <code>pruneKnn</code> function.</dd>


<dt>y</dt>
<dd>List object returned by the <code>compNoise</code> or <code>pruneKnn</code> function (if run with <code>regNB=TRUE</code>).</dd>


<dt>par.nb</dt>
<dd>Parameter to be plotted, i.e. valid column of <code>res$regData$nbRegr</code>.
of the log total UMI count. <code>intercept</code> is the intercept inferred by the regression. Default is <code>NULL</code> and <code>theta</code> is shown.</dd>


<dt>span</dt>
<dd>Positive real number. Parameter for loess-regression (see <code>large</code>) controlling the degree of smoothing. Default is 0.75.</dd>


<dt>...</dt>
<dd>Additional arguments for <code>plot</code>.</dd>

</dl>

plotRegNB: Function for plotting negative binomial regression

Description

Usage

Value

Arguments

Examples