buildPratchet: Wrapper for phangorn::pratchet
In dowser: B Cell Receptor Phylogenetics Toolkit

View source: R/TreeFunctions.R

buildPratchet

R Documentation

Wrapper for phangorn::pratchet

Description

Wrapper for phangorn::pratchet

Usage

buildPratchet(
  clone,
  seq = "sequence",
  asr = "seq",
  asr_thresh = 0.05,
  tree = NULL,
  asr_type = "MPR",
  verbose = 0,
  resolve_random = TRUE,
  data_type = "DNA"
)

Arguments

`clone`	`airrClone` object
`seq`	sequece column in `airrClone` object
`asr`	return sequence or probability matrix?
`asr_thresh`	threshold for including a nucleotide as an alternative
`tree`	fixed tree topology if desired.
`asr_type`	MPR or ACCTRAN
`verbose`	amount of rubbish to print
`resolve_random`	randomly resolve polytomies?
`data_type`	Are sequences DNA or AA?

Value

phylo object created by phangorn::pratchet with nodes attribute containing reconstructed sequences.

dowser documentation built on May 29, 2024, 3:06 a.m.

dowser index

Package overview README.md Building trees with paired heavy and light chain data Build Lineage Trees Discrete Trait Analysis Measurable evolution Plotting Lineage Trees Quickstart Reconstruct Clonal Germlines Reconstruct Intermediate Sequences Build B cell lineage trees Building trees with paired heavy and light chain data Detect ongoing B cell evolution Discrete trait analysis Dowser: Simple lineage tree construction Plot B cell lineage trees Reconstruct clonal germline sequences Reconstruct intermediate sequences

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