buildIgphyml {dowser}

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.