buildIgphyml: Wrapper to build IgPhyML trees and infer intermediate nodes

In dowser: B Cell Receptor Phylogenetics Toolkit

Wrapper to build IgPhyML trees and infer intermediate nodes

Description

Wrapper to build IgPhyML trees and infer intermediate nodes

Usage

buildIgphyml(
  clone,
  igphyml,
  trees = NULL,
  nproc = 1,
  temp_path = NULL,
  id = NULL,
  rseed = NULL,
  quiet = 0,
  rm_files = TRUE,
  rm_dir = NULL,
  partition = c("single", "cf", "hl", "hlf", "hlc", "hlcf"),
  omega = NULL,
  optimize = "lr",
  motifs = "FCH",
  hotness = "e,e,e,e,e,e",
  rates = NULL,
  asrc = 0.95,
  splitfreqs = FALSE,
  ...
)

Arguments

clone	list of airrClone objects
igphyml	igphyml executable
trees	list of tree topologies if desired
nproc	number of cores for parallelization
temp_path	path to temporary directory
id	IgPhyML run id
rseed	random number seed if desired
quiet	amount of rubbish to print
rm_files	remove temporary files?
rm_dir	remove temporary directory?
partition	How to partition omegas along sequences (see details)
omega	omega parameters to estimate (see IgPhyML docs)
optimize	optimize HLP rates (r), lengths (l), topology (t)
motifs	motifs to consider (see IgPhyML docs)
hotness	hotness parameters to estimate (see IgPhyML docs)
rates	comma delimited list showing which omega-defined partitions get a separate rate (e.g. omega=e,e rates=0,1).
asrc	Intermediate sequence cutoff probability
splitfreqs	Calculate codon frequencies on each partition separately?
...	Additional arguments (not currently used)

Details

Partition options in rate order:

• single: 1 omega for whole sequence

• cf: 2 omegas, 1 for all CDRs and 1 for all FWRs

• hl: 2 omegas, 1 for heavy and 1 for light chain

• hlf: 3 omegas, 1 for heavy FWR, 1 for all CDRs, and 1 for light FWRs

• hlc: 3 omegas, 1 for all FWRs, 1 for heavy CDRs, and 1 for light CDRs

• hlcf: 4 omegas, 1 for each heavy FWR, 1 for heavy CDR, 1 for light FWR, and 1 for light CDR

Value

phylo object created by igphyml with nodes attribute containing reconstructed sequences.

dowser documentation built on May 29, 2024, 3:06 a.m.