maxNoisyGenes

This function extracts genes with maximal variability in a cluster or in the entire data set.

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

maxNoisyGenes function

<dl><dt>noise</dt>
<dd>List object with the background noise model and a variability matrix, returned by the <code>compNoise</code> function.</dd>
<dt>cl</dt>
<dd>List object with clustering information, returned by the <code>graphCluster</code> function. Default is <code>NULL</code>.</dd>
<dt>set</dt>
<dd>Postive integer number or vector of integers corresponding to valid cluster numbers. Noise levels are computed across all cells in this subset of clusters. Default is <code>NULL</code> and noise levels are computed across all cells.</dd></dl>

Arguments

Function for extracting genes maximal variability — maxNoisyGenes

<dl>

<dt>noise</dt>
<dd>List object with the background noise model and a variability matrix, returned by the <code>compNoise</code> function.</dd>


<dt>cl</dt>
<dd>List object with clustering information, returned by the <code>graphCluster</code> function. Default is <code>NULL</code>.</dd>


<dt>set</dt>
<dd>Postive integer number or vector of integers corresponding to valid cluster numbers. Noise levels are computed across all cells in this subset of clusters. Default is <code>NULL</code> and noise levels are computed across all cells.</dd>

</dl>

maxNoisyGenes: Function for extracting genes maximal variability

Description

Usage

Value

Arguments

Examples