dfToFasta

Write a fasta file of sequences
<code>readFasta</code> reads a fasta file

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

dfToFasta function

<dl><dt>df</dt>
<dd>dataframe of sequences</dd>
<dt>file</dt>
<dd>FASTA file for output</dd>
<dt>id</dt>
<dd>Column name of sequence ids</dd>
<dt>seq</dt>
<dd>Column name of sequences</dd>
<dt>imgt_gaps</dt>
<dd>Keep IMGT gaps if present?</dd>
<dt>columns</dt>
<dd>vector of column names to append to sequence id</dd></dl>

Arguments

Write a fasta file of sequences
readFasta reads a fasta file — dfToFasta

<dl>

<dt>df</dt>
<dd>dataframe of sequences</dd>


<dt>file</dt>
<dd>FASTA file for output</dd>


<dt>id</dt>
<dd>Column name of sequence ids</dd>


<dt>seq</dt>
<dd>Column name of sequences</dd>


<dt>imgt_gaps</dt>
<dd>Keep IMGT gaps if present?</dd>


<dt>columns</dt>
<dd>vector of column names to append to sequence id</dd>

</dl>

dfToFasta: Write a fasta file of sequences `readFasta` reads a fasta file

Description

Usage

Value

Arguments