airrClone-class

airrClone

<code>airrClone</code> defines a common data structure for perform lineage recontruction
from AIRR data, based heavily on alakazam::ChangeoClone.

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

airrClone-class function

<dl>
<dt><code>data</code></dt>
<dd>data.frame containing sequences and annotations. Contains the
columns <code>sequence_id</code> and <code>sequence</code>, as well as any additional 
sequence-specific annotation columns</dd></dl>
<dt><code>clone</code></dt>
<dd>string defining the clone identifier</dd>
<dt><code>germline</code></dt>
<dd>string containing the heavy chain germline sequence for the clone</dd>
<dt><code>lgermline</code></dt>
<dd>string containing the light chain germline sequence for the clone</dd>
<dt><code>hlgermline</code></dt>
<dd>string containing the combined germline sequence for the clone</dd>
<dt><code>v_gene</code></dt>
<dd>string defining the V segment gene call</dd>
<dt><code>j_gene</code></dt>
<dd>string defining the J segment gene call</dd>
<dt><code>junc_len</code></dt>
<dd>numeric junction length (nucleotide count)</dd>
<dt><code>locus</code></dt>
<dd>index showing which locus represented at each site</dd>
<dt><code>region</code></dt>
<dd>index showing FWR/CDR region for each site</dd>
<dt><code>phylo_seq</code></dt>
<dd>sequence column used for phylogenetic tree building</dd>
<dt><code>numbers</code></dt>
<dd>index (usually IMGT) number of each site in <code>phylo_seq</code></dd>

Slots

S4 class defining a clone in Dowser — airrClone-class

<dl>
<dt><code>data</code></dt>
<dd>data.frame containing sequences and annotations. Contains the
columns <code>sequence_id</code> and <code>sequence</code>, as well as any additional 
sequence-specific annotation columns</dd>


<dt><code>clone</code></dt>
<dd>string defining the clone identifier</dd>


<dt><code>germline</code></dt>
<dd>string containing the heavy chain germline sequence for the clone</dd>


<dt><code>lgermline</code></dt>
<dd>string containing the light chain germline sequence for the clone</dd>


<dt><code>hlgermline</code></dt>
<dd>string containing the combined germline sequence for the clone</dd>


<dt><code>v_gene</code></dt>
<dd>string defining the V segment gene call</dd>


<dt><code>j_gene</code></dt>
<dd>string defining the J segment gene call</dd>


<dt><code>junc_len</code></dt>
<dd>numeric junction length (nucleotide count)</dd>


<dt><code>locus</code></dt>
<dd>index showing which locus represented at each site</dd>


<dt><code>region</code></dt>
<dd>index showing FWR/CDR region for each site</dd>


<dt><code>phylo_seq</code></dt>
<dd>sequence column used for phylogenetic tree building</dd>


<dt><code>numbers</code></dt>
<dd>index (usually IMGT) number of each site in <code>phylo_seq</code></dd>


</dl>

airrClone-class: S4 class defining a clone in Dowser

Description

Arguments

Slots

See Also