quantKnn

This function computes a number of noise-related quantities for all pruned k-nearest neighbourhoods.

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

quantKnn function

<dl><dt>res</dt>
<dd>List object with k nearest neighbour information returned by <code>pruneKnn</code> function.</dd>
<dt>noise</dt>
<dd>List of noise parameters returned by <code>compTBNoise</code>.</dd>
<dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>pvalue</dt>
<dd>Positive real number between 0 and 1. All nearest neighbours with link probability <code>&lt; pvalue</code> are discarded. Default is 0.01.</dd>
<dt>minN</dt>
<dd>Positive integer number. Noise inference is only done for k-nearest neighbourhoods with at least <code>minN</code> neighbours remaining after pruning.</dd>
<dt>no_cores</dt>
<dd>Positive integer number. Number of cores for multithreading. If set to <code>NULL</code> then the number of available cores minus two is used. Default is <code>NULL</code>.</dd></dl>

Arguments

Noise-related quantaties of local pruned k-nearest neighbourhoods — quantKnn

<dl>

<dt>res</dt>
<dd>List object with k nearest neighbour information returned by <code>pruneKnn</code> function.</dd>


<dt>noise</dt>
<dd>List of noise parameters returned by <code>compTBNoise</code>.</dd>


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


<dt>pvalue</dt>
<dd>Positive real number between 0 and 1. All nearest neighbours with link probability <code>&lt; pvalue</code> are discarded. Default is 0.01.</dd>


<dt>minN</dt>
<dd>Positive integer number. Noise inference is only done for k-nearest neighbourhoods with at least <code>minN</code> neighbours remaining after pruning.</dd>


<dt>no_cores</dt>
<dd>Positive integer number. Number of cores for multithreading. If set to <code>NULL</code> then the number of available cores minus two is used. Default is <code>NULL</code>.</dd>

</dl>

quantKnn: Noise-related quantaties of local pruned k-nearest neighbourhoods

Description

Usage

Value

Arguments