readTreesJSON

<code>readTreesJSON</code>
Experimental. Read trees from JSON/AIRR format from Dowser

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

readTreesJSON function

<dl><dt>file</dt>
<dd>.json file</dd>
<dt>heavy</dt>
<dd>name of heavy chain locus</dd>
<dt>light</dt>
<dd>names of light chain loci</dd>
<dt>verbose</dt>
<dd>how much info to print</dd>
<dt>edge_tol</dt>
<dd>tolerance for branch length checks (if check=TRUE)</dd>
<dt>nproc</dt>
<dd>number of cores to use (parallelizes by clone)</dd></dl>

Arguments

readTreesJSON
Experimental. Read trees from JSON/AIRR format from Dowser — readTreesJSON

<dl>

<dt>file</dt>
<dd>.json file</dd>


<dt>heavy</dt>
<dd>name of heavy chain locus</dd>


<dt>light</dt>
<dd>names of light chain loci</dd>


<dt>verbose</dt>
<dd>how much info to print</dd>


<dt>edge_tol</dt>
<dd>tolerance for branch length checks (if check=TRUE)</dd>


<dt>nproc</dt>
<dd>number of cores to use (parallelizes by clone)</dd>

</dl>

readTreesJSON: `readTreesJSON` Experimental. Read trees from JSON/AIRR format from Dowser

Description

Usage

Arguments

Details