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,
...
)
Arguments¶
- clone
- list of
airrCloneobjects - 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)
Value¶
phylo object created by igphyml with nodes attribute
containing reconstructed sequences.
Details¶
Partition options in rate order:
single: 1 omega for whole sequencecf: 2 omegas, 1 for all CDRs and 1 for all FWRshl: 2 omegas, 1 for heavy and 1 for light chainhlf: 3 omegas, 1 for heavy FWR, 1 for all CDRs, and 1 for light FWRshlc: 3 omegas, 1 for all FWRs, 1 for heavy CDRs, and 1 for light CDRshlcf: 4 omegas, 1 for each heavy FWR, 1 for heavy CDR, 1 for light FWR, and 1 for light CDR