filterPartialSeqs

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

filterPartialSeqs function

<dl><dt>data</dt>
<dd>Data table of sequences (preferably in AIRR format)</dd>
<dt>seq</dt>
<dd>name of sequence column for filtering</dd>
<dt>cutoff</dt>
<dd>number of matches to the <code>pattern</code> option required</dd>
<dt>pattern</dt>
<dd>regex for matching (defaults to A, T, C, or G)</dd>
<dt>verbose</dt>
<dd>print out number of seqs removed
data(ExampleAirr)
filtered = filterPartialSeqs(ExampleAirr)</dd></dl>

Arguments

filterPartialSeqs — filterPartialSeqs

<dl>

<dt>data</dt>
<dd>Data table of sequences (preferably in AIRR format)</dd>


<dt>seq</dt>
<dd>name of sequence column for filtering</dd>


<dt>cutoff</dt>
<dd>number of matches to the <code>pattern</code> option required</dd>


<dt>pattern</dt>
<dd>regex for matching (defaults to A, T, C, or G)</dd>


<dt>verbose</dt>
<dd>print out number of seqs removed
data(ExampleAirr)
filtered = filterPartialSeqs(ExampleAirr)</dd>

</dl>

<code>filterPartialSeqs</code>

filterPartialSeqs: `filterPartialSeqs`

Description

Usage

Arguments