cleanNN

This function compares the neighborhood of a cell with the neighorhoods of all of its k nearest neighors and prunes links to neighbors that do not co-occur in a defined minimum number of neighborhoods by setting their link p-value (entry in <code>pvM</code> data.frame of <code>res</code> input object) to 0.

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

cleanNN function

<dl><dt>res</dt>
<dd>List object with k nearest neighbour information returned by <code>pruneKnn</code> function.</dd>
<dt>minN</dt>
<dd>Positive integer number. Minimum of neighborhoods across the k nearest neighbours of a cell expected to share a neighbor with the cell. Default is 2.</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

Function for pruning k-nearest neighborhoods based on neighborhood overlap — cleanNN

<dl>

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


<dt>minN</dt>
<dd>Positive integer number. Minimum of neighborhoods across the k nearest neighbours of a cell expected to share a neighbor with the cell. Default is 2.</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>

cleanNN: Function for pruning k-nearest neighborhoods based on neighborhood overlap

Description

Usage

Value

Arguments