calculate_GBLD: Calculate the GBLD distance between trees in an...

In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

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

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

Usage

calculate_GBLD(AntibodyForests_object, min.nodes)

Arguments

AntibodyForests_object	AntibodyForests-object, output from AntibodyForests()
min.nodes	integer - The minimum number of nodes (including the germline) in a tree to include in the analysis. Default is 3.

Value

A matrix with the GBLD distances between trees in the AntibodyForests object.

Examples

GBLD_matrix <- calculate_GBLD(AntibodyForests_object = AntibodyForests::small_af)
GBLD_matrix[1:5, 1:5]

AntibodyForests documentation built on April 4, 2025, 4:45 a.m.