buildIgphyml - Wrapper to build IgPhyML trees and infer intermediate nodes
Wrapper to build IgPhyML trees and infer intermediate nodes
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, ... )
- list of
- igphyml executable
- list of tree topologies if desired
- number of cores for parallelization
- path to temporary directory
- IgPhyML run id
- random number seed if desired
- amount of rubbish to print
- remove temporary files?
- remove temporary directory?
- How to partition omegas along sequences (see details)
- omega parameters to estimate (see IgPhyML docs)
- optimize HLP rates (r), lengths (l), topology (t)
- motifs to consider (see IgPhyML docs)
- hotness parameters to estimate (see IgPhyML docs)
- comma delimited list showing which omega-defined partitions get a separate rate (e.g. omega=e,e rates=0,1).
- Intermediate sequence cutoff probability
- Calculate codon frequencies on each partition separately?
- Additional arguments (not currently used)
phylo object created by igphyml with nodes attribute
containing reconstructed sequences.
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