buildIgphyml: 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,
  ...
)

Value

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

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