writeLineageFile - Write lineage file for IgPhyML use

Description¶

Write lineage file for IgPhyML use

Usage¶

writeLineageFile(
data,
trees = NULL,
dir = ".",
id = "N",
rep = NULL,
trait = NULL,
empty = TRUE,
partition = "single",
heavy = "IGH",
...
)

Arguments¶

data

list of airrClone objects

trees

list of phylo objects corresponding to data

dir

directory to write file

id

id used for IgPhyML run

rep

bootstrap replicate

trait

string appended to sequence id in fasta files

empty

output uninformative sequences?

partition

how to partition omegas

heavy

name of heavy chain locus

…

additional arguments to be passed

Value¶

Name of created lineage file.