comppvalue

This function computes a p-value for the significance (i.e. over-representation of assigned cells) of each inter-cluster link.

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

comppvalue function

<dl><dt>object</dt>
<dd><code>Ltree</code> class object.</dd>
<dt>pthr</dt>
<dd>p-value cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells.</dd>
<dt>sensitive</dt>
<dd>logical. Only relevant when <code>nmode=TRUE</code> in function <code>projcell</code>. If <code>TRUE</code>, then all cells on the most highly significant link are
and the link itself are disregard to test significance of the remaining links with a binomial p-value. Default is <code>FALSE</code>.</dd></dl>

Arguments

Computing P-values for Link Significance — comppvalue

<dl>

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


<dt>pthr</dt>
<dd>p-value cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells.</dd>


<dt>sensitive</dt>
<dd>logical. Only relevant when <code>nmode=TRUE</code> in function <code>projcell</code>. If <code>TRUE</code>, then all cells on the most highly significant link are
and the link itself are disregard to test significance of the remaining links with a binomial p-value. Default is <code>FALSE</code>.</dd>

</dl>

comppvalue: Computing P-values for Link Significance

Description

Usage

Value

Arguments

Examples