collapseNodes

<code>collapseNodes</code> Node collapsing function.

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

collapseNodes function

<dl><dt>trees</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of getTrees</dd>
<dt>tips</dt>
<dd>collapse tips to internal nodes? (experimental)</dd>
<dt>check</dt>
<dd>check that collapsed nodes are consistent with original tree</dd></dl>

Arguments

Collapse internal nodes with the same predicted sequence — collapseNodes

<dl>

<dt>trees</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of getTrees</dd>


<dt>tips</dt>
<dd>collapse tips to internal nodes? (experimental)</dd>


<dt>check</dt>
<dd>check that collapsed nodes are consistent with original tree</dd>

</dl>

collapseNodes: Collapse internal nodes with the same predicted sequence

Description

Usage

Value

Arguments

Details

See Also