calculate_GBLD

Calculate the GBLD distance between trees in an AntibodyForests object. Code is derived from https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb

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

calculate_GBLD function

<dl><dt>AntibodyForests_object</dt>
<dd>AntibodyForests-object, output from AntibodyForests()</dd>
<dt>min.nodes</dt>
<dd><ul>
<li>integer - The minimum number of nodes (including the germline) in a tree to include in the analysis. Default is 3.</li>
</ul></dd></dl>

Arguments

Calculate the GBLD distance between trees in an AntibodyForests object. Code is derived from https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb
Farnia, M., Tahiri, N. New generalized metric based on branch length distance to compare B cell lineage trees. Algorithms Mol Biol 19, 22 (2024). https://doi.org/10.1186/s13015-024-00267-1 — calculate_GBLD

<dl>

<dt>AntibodyForests_object</dt>
<dd>AntibodyForests-object, output from AntibodyForests()</dd>


<dt>min.nodes</dt>
<dd><ul>
<li>integer - The minimum number of nodes (including the germline) in a tree to include in the analysis. Default is 3.</li>
</ul></dd>

</dl>

Calculate the GBLD distance between trees in an AntibodyForests object. Code is derived from https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb
Farnia, M., Tahiri, N. New generalized metric based on branch length distance to compare B cell lineage trees. Algorithms Mol Biol 19, 22 (2024). https://doi.org/10.1186/s13015-024-00267-1

Description

Usage

Value

Arguments

Examples