writeLineageFile

Write lineage file for IgPhyML use

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

writeLineageFile function

<dl><dt>data</dt>
<dd>list of <code>airrClone</code> objects</dd>
<dt>trees</dt>
<dd>list of <code>phylo</code> objects corresponding to <code>data</code></dd>
<dt>dir</dt>
<dd>directory to write file</dd>
<dt>id</dt>
<dd>id used for IgPhyML run</dd>
<dt>rep</dt>
<dd>bootstrap replicate</dd>
<dt>trait</dt>
<dd>string appended to sequence id in fasta files</dd>
<dt>empty</dt>
<dd>output uninformative sequences?</dd>
<dt>partition</dt>
<dd>how to partition omegas</dd>
<dt>heavy</dt>
<dd>name of heavy chain locus</dd></dl>

Arguments

Write lineage file for IgPhyML use — writeLineageFile

<dl>

<dt>data</dt>
<dd>list of <code>airrClone</code> objects</dd>


<dt>trees</dt>
<dd>list of <code>phylo</code> objects corresponding to <code>data</code></dd>


<dt>dir</dt>
<dd>directory to write file</dd>


<dt>id</dt>
<dd>id used for IgPhyML run</dd>


<dt>rep</dt>
<dd>bootstrap replicate</dd>


<dt>trait</dt>
<dd>string appended to sequence id in fasta files</dd>


<dt>empty</dt>
<dd>output uninformative sequences?</dd>


<dt>partition</dt>
<dd>how to partition omegas</dd>


<dt>heavy</dt>
<dd>name of heavy chain locus</dd>

</dl>

writeLineageFile: Write lineage file for IgPhyML use

Description

Usage

Value

Arguments