createKnnMatrix

This creates an adjacency matrix, keeping only nearest neighbour with a link probability above a minimum probability

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

createKnnMatrix function

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

Arguments

Function to create a knn matrix — createKnnMatrix

<dl>

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

</dl>

createKnnMatrix: Function to create a knn matrix

Description

Usage

Value

Arguments

Examples