getBootstraps - 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
airrCloneobjects, 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
igphymlordnaparsspecified) - id
- unique identifer for this analysis (required if
igphymlordnaparsspecified) - 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
Value¶
The input clones tibble with an additional column for the bootstrap replicate trees.