getDiffPoint

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

getDiffPoint function

<dl><dt>tree</dt>
<dd>a treedata object, from getTimeTrees</dd>
<dt>targetnode</dt>
<dd>current node</dd>
<dt>trait</dt>
<dd>column name of the trait of interest</dd>
<dt>height</dt>
<dd>which height value to return</dd>
<dt>verbose</dt>
<dd>print out run info</dd>
<dt>eo_adjust</dt>
<dd>adjust heights using expectOccupancies (recommended, requires eo_type)</dd>
<dt>eo_type</dt>
<dd>if eo_adjust, trait value described by expectedOccupancies (typically state 1 of 2)</dd></dl>

Arguments

Recurse up to tree to find most recent node with different state, or the root — getDiffPoint

<dl>

<dt>tree</dt>
<dd>a treedata object, from getTimeTrees</dd>


<dt>targetnode</dt>
<dd>current node</dd>


<dt>trait</dt>
<dd>column name of the trait of interest</dd>


<dt>height</dt>
<dd>which height value to return</dd>


<dt>verbose</dt>
<dd>print out run info</dd>


<dt>eo_adjust</dt>
<dd>adjust heights using expectOccupancies (recommended, requires eo_type)</dd>


<dt>eo_type</dt>
<dd>if eo_adjust, trait value described by expectedOccupancies (typically state 1 of 2)</dd>

</dl>

Recurse up to tree to find most recent node with different state, or the root

getDiffPoint: Recurse up to tree to find most recent node with different state, or the root

Description

Usage

Arguments