dowser (version 2.5.1)

writeTreesJSON: writeTreesJSON Experimental. Write trees in AIRR format

Description

writeTreesJSON Experimental. Write trees in AIRR format

Usage

writeTreesJSON(
  object,
  file,
  repertoire_id = "sample",
  check = TRUE,
  verbose = TRUE,
  edge_tol = 1e-08,
  cell = "cell_id",
  heavy = "IGH",
  light = c("IGK", "IGL"),
  dowser_fields = TRUE,
  nproc = 1
)

Arguments

object

Dowser object from getTrees

file

name of .json file

repertoire_id

repertoire_id to use

check

verify object is equivalent on reloading

verbose

print out more info

edge_tol

tolerance for branch length checks (if check=TRUE)

cell

cell id column name in Dowser object

heavy

name of heavy chain locus

light

names of light chain loci

dowser_fields

include dowser-specific information? (recommended)

nproc

number of cores to use (parallelizes by clone)

Details

Works with trees built by any of getTrees's build options ("pratchet", "pml", "igphyml", "raxml"). getTrees(..., build="pml") trees store the full phangorn::optim.pml fit in tree$parameters; since that object isn't JSON-serializable (and isn't meaningful to reconstruct from a file), it's reduced to a flat list of fitted model parameters via pmlParamsToList before being written out. See that function's documentation for what is kept and why.