buildPratchet

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

buildPratchet function

<dl><dt>clone</dt>
<dd><code>airrClone</code> object</dd>
<dt>seq</dt>
<dd>sequece column in <code>airrClone</code> object</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>asr_type</dt>
<dd>MPR or ACCTRAN</dd>
<dt>verbose</dt>
<dd>amount of rubbish to print</dd>
<dt>resolve_random</dt>
<dd>randomly resolve polytomies?</dd>
<dt>data_type</dt>
<dd>Are sequences DNA or AA?</dd></dl>

Arguments

Wrapper for phangorn::pratchet — buildPratchet

<dl>

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


<dt>seq</dt>
<dd>sequece column in <code>airrClone</code> object</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>asr_type</dt>
<dd>MPR or ACCTRAN</dd>


<dt>verbose</dt>
<dd>amount of rubbish to print</dd>


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


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

</dl>

Wrapper for phangorn::pratchet

buildPratchet: Wrapper for phangorn::pratchet

Description

Usage

Value

Arguments