bootstrapTrees

bootstrapTrees - Create a bootstrap distribution for clone sequence alignments, and estimate trees for each bootstrap replicate.

Description¶

bootstrapTrees Phylogenetic bootstrap function.

Usage¶

bootstrapTrees(
clones,
bootstraps,
nproc = 1,
trait = NULL,
dir = NULL,
id = NULL,
modelfile = NULL,
build = "pratchet",
exec = NULL,
igphyml = NULL,
fixtrees = FALSE,
quiet = 0,
rm_temp = TRUE,
palette = NULL,
resolve = 2,
rep = NULL,
keeptrees = TRUE,
lfile = NULL,
seq = "sequence",
downsample = FALSE,
tip_switch = 20,
...
)

Arguments¶

clones: tibble airrClone objects, the output of formatClones
bootstraps: number of bootstrap replicates to perform
nproc: number of cores to parallelize computations
trait: trait to use for parsimony models (required if igphyml specified)
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)
modelfile: file specifying parsimony model to use
build: program to use for tree building (phangorn, dnapars)
exec: location of desired phylogenetic executable
igphyml: location of igphyml executible if trait models desired
fixtrees: keep tree topologies fixed? (bootstrapping will not be perfomed)
quiet: amount of rubbish to print to console
rm_temp: remove temporary files (default=TRUE)
palette: a named vector specifying colors for each state
resolve: how should polytomies be resolved?
rep: current bootstrap replicate (experimental)
keeptrees: keep trees estimated from bootstrap replicates? (TRUE)
lfile: lineage file input to igphyml if desired (experimental)
seq: column name containing sequence information
downsample: downsample clones to have a maximum specified tip/switch ratio?
tip_switch: maximum allowed tip/switch ratio if downsample=TRUE
…: additional arguments to be passed to tree building program

Value¶

A list of trees and/or switch counts for each bootstrap replicate.

Details¶

Tree building details are the same as getTrees. If keeptrees=TRUE (default) the returned object will contain a list named “trees” which contains a list of estimated tree objects for each bootstrap replicate. The object is structured like: trees[[]][[]]. If igphyml is specified (as well as trait), the returned object will contain a tibble named “switches” containing switch count information. This object can be passed to testSP and other functions to perform parsimony based trait value tests.

Examples¶

### Not run:
data(ExampleAirr)
# ExampleAirr$sample_id <- sample(ExampleAirr$sample_id)
# clones <- formatClones(ExampleAirr, trait="sample_id")
# 
# igphyml <- "~/apps/igphyml/src/igphyml"
# btrees <- bootstrapTrees(clones[1:2], bootstraps=10, nproc=1,
# igphyml=igphyml, trait="sample_id")
# plotTrees(btrees$trees[[4]])[[1]]
# testPS(btrees$switches)