downsampleClone

<code>downsampleClone</code> Down-sample clone to maximum tip/switch ratio

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

downsampleClone function

<dl><dt>clone</dt>
<dd>an airrClone object</dd>
<dt>trait</dt>
<dd>trait considered for rarefaction
getTrees</dd>
<dt>tip_switch</dt>
<dd>maximum tip/switch ratio</dd>
<dt>tree</dt>
<dd>a <code>phylo</code> tree object correspond to <code>clone</code></dd></dl>

Arguments

downsampleClone Down-sample clone to maximum tip/switch ratio — downsampleClone

<dl>

<dt>clone</dt>
<dd>an airrClone object</dd>


<dt>trait</dt>
<dd>trait considered for rarefaction
getTrees</dd>


<dt>tip_switch</dt>
<dd>maximum tip/switch ratio</dd>


<dt>tree</dt>
<dd>a <code>phylo</code> tree object correspond to <code>clone</code></dd>

</dl>

downsampleClone: `downsampleClone` Down-sample clone to maximum tip/switch ratio

Description

Usage

Value

Arguments