getTreesAndUCAs: getTreesAndUCAs Construct trees and infer the UCA

In dowser: B Cell Receptor Phylogenetics Toolkit

getTreesAndUCAs Construct trees and infer the UCA

Description

getTreesAndUCAs Construct trees and infer the UCA

Usage

getTreesAndUCAs(
  clones,
  data,
  exec,
  model_folder,
  references,
  dir = NULL,
  model_folder_igk = NULL,
  model_folder_igl = NULL,
  partition = "single",
  repertoire_wide = FALSE,
  python = "python3",
  id = "sample",
  max_iters = 100,
  nproc = 1,
  rm_temp = TRUE,
  quiet = 0,
  chain = "H",
  clone = "clone_id",
  cell = "cell_id",
  subsample_size = NA,
  subsampling_method = c("random", "weighted", "least_mutated"),
  search = c("codon", "nt"),
  resolve_vj = FALSE,
  fix_vj_in_cdr3 = TRUE,
  fill_partials = TRUE,
  split_light = FALSE,
  ...
)

Arguments

clones	AIRR-table containing sequences formatClones
data	The AIRR-table that was used to make the clones object.
exec	File path to the tree building executable
model_folder	The file path to the OLGA default model files for heavy chains
references	Reference genes. See readIMGT
dir	The file path of the directory of where data is saved. NULL is default.
model_folder_igk	The file path to the OLGA default model files for IGK
model_folder_igl	The file path to the OLGA default model files for IGL
partition	The partition model to use with IgPhyML. "single" is the default.
repertoire_wide	Build trees using parameters inferred from the entire dataset?
python	Specify the python call for your system. This is the call on command line that issues the python you want to use. "python3" by default.
id	The run ID, sample by default
max_iters	The maximum number of iterations to run before ending. 100 by default
nproc	The number of cores to use
rm_temp	Remove the generated files?
quiet	Amount of noise to print out
chain	Set to HL to use both heavy and light chain sequences
clone	The name of the clone id column used in formatClones.
cell	The name of the cell id in the AIRR table used to generate formatClones
subsample_size	The amount that the clone should be sampled down to. By default this is NA to not induce subsampling.
subsampling_method	How to subsample. Methods include 'random', 'weighted', and 'least_mutated'. The later two methods require 'mu_freq' to be passed as a trait when running
search	Search codon or nt space
resolve_vj	Resolve the V and J gene annotations within each clone?
fix_vj_in_cdr3	Check if the inferred V/J lengths go into the inferred cdr3 region and adjust accordingly.
fill_partials	A logical that will fill in the V and J UCAs of clones that have partial V/J sequence alignments
split_light	A logical that indicates if different light chain groups should be used to further split a clone (recommended for paired data)
...	Additional arguments passed to various other functions like getTrees and buildGermline

Details

Return object adds/edits following columns:

• trees: The phylogenies associated with each clone

• UCA: The inferred UCA

Value

An airrClone object with trees and the inferred UCA

See Also

getTrees

dowser documentation built on Aug. 20, 2026, 5:06 p.m.