newick_to_Af

Converts files with phylogenetic trees in newick format into an AntibodyForests object. Make sure that the germline node is called "germline" and that every line represents a new tree in the newick file. All trees in the same file should be from the same sample.

The generated wealth of immune repertoire sequencing data
requires software to investigate and quantify inter- and
intra-antibody repertoire evolution to uncover how B cells evolve
during immune responses. Here, we present 'AntibodyForests', a software
to investigate and quantify inter- and intra-antibody repertoire
evolution.

Alexander Yermanos

AntibodyForests

Delineating Inter- And Intra-Antibody Repertoire Evolution

Daphne van Ginneken

Valentijn Tromp

Tudor-Stefan Cotet

newick_to_Af function

<dl><dt>file.list</dt>
<dd>list - list of newick files to be converted to AntibodyForests object. Could be a named list where the names correspond to sample IDs.</dd>
<dt>file.dir</dt>
<dd>directory - directory where the newick files are stored. If provided, the function will read all newick files in the directory.</dd></dl>

Arguments

Converts files with phylogenetic trees in newick format into an AntibodyForests object. — newick_to_Af

<dl>

<dt>file.list</dt>
<dd>list - list of newick files to be converted to AntibodyForests object. Could be a named list where the names correspond to sample IDs.</dd>


<dt>file.dir</dt>
<dd>directory - directory where the newick files are stored. If provided, the function will read all newick files in the directory.</dd>

</dl>

newick_to_Af: Converts files with phylogenetic trees in newick format into an AntibodyForests object.

Description

Usage

Value

Arguments

Examples