buildIgphyml {dowser} | R Documentation |
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 = "e",
optimize = "lr",
motifs = "FCH",
hotness = "e,e,e,e,e,e",
rates = NULL,
asrc = 0.95,
splitfreqs = FALSE,
...
)
clone |
list of |
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) |
Partition options:
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 all CDRs, 2 for heavy/light FWRs
hlc
: 3 omegas, 1 for all FWRs, 2 for heavy/light CDRs
hlcf
: 4 omegas, 1 for each heavy/light CDR/FWR combination
phylo
object created by igphyml with nodes attribute
containing reconstructed sequences.