create_starting_tree

Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree

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

create_starting_tree function

<dl><dt>clone</dt>
<dd>an <code>airrClone</code> object</dd>
<dt>id</dt>
<dd>unique identifer for this analysis</dd>
<dt>tree</dt>
<dd>starting tree, either a phylo object or a newick string</dd>
<dt>include_germline_as_tip</dt>
<dd>include the germline as a tip</dd>
<dt>tree_states</dt>
<dd>use states in the starting tree?</dd>
<dt>start_edge_length</dt>
<dd>edge length to use for all branches in starting tree</dd></dl>

Arguments

Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree — create_starting_tree

<dl>

<dt>clone</dt>
<dd>an <code>airrClone</code> object</dd>


<dt>id</dt>
<dd>unique identifer for this analysis</dd>


<dt>tree</dt>
<dd>starting tree, either a phylo object or a newick string</dd>


<dt>include_germline_as_tip</dt>
<dd>include the germline as a tip</dd>


<dt>tree_states</dt>
<dd>use states in the starting tree?</dd>


<dt>start_edge_length</dt>
<dd>edge length to use for all branches in starting tree</dd>

</dl>

create_starting_tree: Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree

Description

Usage

Value

Arguments