getAllSeqs

<code>getNodeSeq</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

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

getAllSeqs function

<dl><dt>data</dt>
<dd>a tibble of <code>airrClone</code> objects with reconstructed trees, 
the output of getTrees</dd>
<dt>imgt_gaps</dt>
<dd>include a column of gapped sequences?</dd></dl>

Arguments

Return all tip and internal node sequences — getAllSeqs

<dl>

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


<dt>imgt_gaps</dt>
<dd>include a column of gapped sequences?</dd>

</dl>

getAllSeqs: Return all tip and internal node sequences

Description

Usage

Value

Arguments

Details

See Also