stopCodonCheck

Check whether sequences have in-frame premature stop codons (PTCs)

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

stopCodonCheck function

<dl><dt>sequences</dt>
<dd>Vector of nucleotide sequences in desired reading frame</dd>
<dt>nproc</dt>
<dd>Number of cores for preprocessing</dd>
<dt>check</dt>
<dd>Check whether codons split correctly</dd></dl>

Arguments

Check whether sequences have in-frame premature stop codons (PTCs) — stopCodonCheck

<dl>

<dt>sequences</dt>
<dd>Vector of nucleotide sequences in desired reading frame</dd>


<dt>nproc</dt>
<dd>Number of cores for preprocessing</dd>


<dt>check</dt>
<dd>Check whether codons split correctly</dd>

</dl>

stopCodonCheck: Check whether sequences have in-frame premature stop codons (PTCs)

Description

Usage

Value

Arguments