getSeqPath

Return all sequences along the tree from the germline to a specified node

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

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Erick Matsen

Steven Kleinstein

getSeqPath 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>
<dt>translate</dt>
<dd>Tranlate into amino acids?</dd>
<dt>rm_x_aa</dt>
<dd>Remove amino acids translated to X</dd>
<dt>dot_notation</dt>
<dd>Represent sites with germline character as "." and ambiguous sites as "?"</dd>
<dt>verbose</dt>
<dd>print out extra information?</dd></dl>

Arguments

Return all sequences along the tree from the germline to a specified node — getSeqPath

<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>


<dt>translate</dt>
<dd>Tranlate into amino acids?</dd>


<dt>rm_x_aa</dt>
<dd>Remove amino acids translated to X</dd>


<dt>dot_notation</dt>
<dd>Represent sites with germline character as "." and ambiguous sites as "?"</dd>


<dt>verbose</dt>
<dd>print out extra information?</dd>

</dl>

getSeqPath: Return all sequences along the tree from the germline to a specified node

Description

Usage

Value

Arguments

See Also