getSeq

<code>getSeq</code> Sequence retrieval function.

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

getSeq function

<dl><dt>data</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of
getTrees</dd>
<dt>node</dt>
<dd>numeric node in tree (see details)</dd>
<dt>tree</dt>
<dd>a <code>phylo</code> tree object containing <code>node</code></dd>
<dt>clone</dt>
<dd>if <code>tree</code> not specified, supply clone ID in <code>data</code></dd>
<dt>gaps</dt>
<dd>add IMGT gaps to output sequences?</dd></dl>

Arguments

Deprecated! Use getNodeSeq — getSeq

<dl>

<dt>data</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of
getTrees</dd>


<dt>node</dt>
<dd>numeric node in tree (see details)</dd>


<dt>tree</dt>
<dd>a <code>phylo</code> tree object containing <code>node</code></dd>


<dt>clone</dt>
<dd>if <code>tree</code> not specified, supply clone ID in <code>data</code></dd>


<dt>gaps</dt>
<dd>add IMGT gaps to output sequences?</dd>

</dl>

getSeq: Deprecated! Use getNodeSeq

Description

Usage

Value

Arguments

See Also