compscore

This function extracts the number of links connecting a given cluster to other cluster, the delta median entropy of each cluster
(median entropy of a cluster after subtracting the minimum median entropy across all clusters), and the StemID2 score which is the product of both quantities for
each cluster.

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

compscore function

<dl><dt>object</dt>
<dd><code>Ltree</code> class object.</dd>
<dt>nn</dt>
<dd>Positive integer number. Number of higher order neighbors to be included for the determination of links: indirect connections via <code>n-1</code> intermittant
neighbors are allowed. Default is 1.</dd>
<dt>scthr</dt>
<dd>Real number between zero and one. Score threshold for links to be included in the calculation. For <code>scthr=0</code> all significant links are included. The
maximum score is one.</dd>
<dt>show</dt>
<dd>logical. If <code>TRUE</code>, then plot heatmap of projections. Default is <code>TRUE</code>.</dd></dl>

Arguments

Compute StemID2 score — compscore

<dl>

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


<dt>nn</dt>
<dd>Positive integer number. Number of higher order neighbors to be included for the determination of links: indirect connections via <code>n-1</code> intermittant
neighbors are allowed. Default is 1.</dd>


<dt>scthr</dt>
<dd>Real number between zero and one. Score threshold for links to be included in the calculation. For <code>scthr=0</code> all significant links are included. The
maximum score is one.</dd>


<dt>show</dt>
<dd>logical. If <code>TRUE</code>, then plot heatmap of projections. Default is <code>TRUE</code>.</dd>

</dl>

compscore: Compute StemID2 score

Description

Usage

Value

Arguments