buildPML

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

buildPML function

<dl><dt>clone</dt>
<dd><code>airrClone</code> object</dd>
<dt>seq</dt>
<dd>sequece column in <code>airrClone</code> object</dd>
<dt>sub_model</dt>
<dd>substitution model to use</dd>
<dt>gamma</dt>
<dd>gamma site rate variation?</dd>
<dt>asr</dt>
<dd>return sequence or probability matrix?</dd>
<dt>asr_thresh</dt>
<dd>threshold for including a nucleotide as an alternative</dd>
<dt>tree</dt>
<dd>fixed tree topology if desired.</dd>
<dt>data_type</dt>
<dd>Are sequences DNA or AA?</dd>
<dt>optNni</dt>
<dd>Optimize tree topology</dd>
<dt>optQ</dt>
<dd>Optimize Q matrix</dd>
<dt>verbose</dt>
<dd>Print error messages as they happen?</dd>
<dt>resolve_random</dt>
<dd>randomly resolve polytomies?</dd>
<dt>quiet</dt>
<dd>amount of rubbish to print to console</dd>
<dt>rep</dt>
<dd>current bootstrap replicate (experimental)</dd></dl>

Arguments

Wrapper for phangorn::optim.pml — buildPML

<dl>

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


<dt>seq</dt>
<dd>sequece column in <code>airrClone</code> object</dd>


<dt>sub_model</dt>
<dd>substitution model to use</dd>


<dt>gamma</dt>
<dd>gamma site rate variation?</dd>


<dt>asr</dt>
<dd>return sequence or probability matrix?</dd>


<dt>asr_thresh</dt>
<dd>threshold for including a nucleotide as an alternative</dd>


<dt>tree</dt>
<dd>fixed tree topology if desired.</dd>


<dt>data_type</dt>
<dd>Are sequences DNA or AA?</dd>


<dt>optNni</dt>
<dd>Optimize tree topology</dd>


<dt>optQ</dt>
<dd>Optimize Q matrix</dd>


<dt>verbose</dt>
<dd>Print error messages as they happen?</dd>


<dt>resolve_random</dt>
<dd>randomly resolve polytomies?</dd>


<dt>quiet</dt>
<dd>amount of rubbish to print to console</dd>


<dt>rep</dt>
<dd>current bootstrap replicate (experimental)</dd>

</dl>

Wrapper for phangorn::optim.pml

buildPML: Wrapper for phangorn::optim.pml

Description

Usage

Value

Arguments