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

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

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

Description

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.

Usage

newick_to_Af(file.list, file.dir)

Arguments

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

Value

AntibodyForests object

Examples

## Not run: 
af <- newick_to_Af(file.list = list("S1" = "path/to/sample1.nwk", "S2" = "path/to/sample2.nwk"))

## End(Not run)

AntibodyForests documentation built on Aug. 8, 2025, 6:49 p.m.