getBootstraps: Creates a bootstrap distribution for clone sequence...
In dowser: B Cell Receptor Phylogenetics Toolkit

getBootstraps

R Documentation

Creates a bootstrap distribution for clone sequence alignments, and returns estimated trees for each bootstrap replicate as a nested list as a new input tibble column.

Description

getBootstraps Phylogenetic bootstrap function.

Usage

getBootstraps(
  clones,
  bootstraps,
  nproc = 1,
  bootstrap_nodes = TRUE,
  dir = NULL,
  id = NULL,
  build = "pratchet",
  exec = NULL,
  quiet = 0,
  rm_temp = TRUE,
  rep = NULL,
  seq = NULL,
  boot_part = "locus",
  by_codon = TRUE,
  starting_tree = FALSE,
  switches = FALSE,
  ...
)

Arguments

`clones`	tibble `airrClone` objects, the output of formatClones
`bootstraps`	number of bootstrap replicates to perform
`nproc`	number of cores to parallelize computations
`bootstrap_nodes`	a logical if the the nodes for each tree in the trees column (required) should report their bootstrap value
`dir`	directory where temporary files will be placed (required if `igphyml` or `dnapars` specified)
`id`	unique identifer for this analysis (required if `igphyml` or `dnapars` specified)
`build`	program to use for tree building (phangorn, dnapars, igphyml)
`exec`	location of desired phylogenetic executable
`quiet`	amount of rubbish to print to console
`rm_temp`	remove temporary files (default=TRUE)
`rep`	current bootstrap replicate (experimental)
`seq`	column name containing sequence information
`boot_part`	is "locus" bootstrap columns for each locus separately
`by_codon`	a logical if the user wants to bootstrap by codon or by nucleotide. Default (codon based bootstrapping) is TRUE.
`starting_tree`	An indicator to use the existing trees column as the starting trees for RAxML
`switches`	a logical indicator to allow findSwitches to do permutations.
`...`	additional arguments to be passed to tree building program