getSeqPath: Return all sequences along the tree from the germline to a...

In dowser: B Cell Receptor Phylogenetics Toolkit

Return all sequences along the tree from the germline to a specified node

Description

Return all sequences along the tree from the germline to a specified node

Usage

getSeqPath(
  data,
  node,
  tree = NULL,
  clone = NULL,
  gaps = TRUE,
  translate = FALSE,
  rm_x_aa = FALSE,
  dot_notation = FALSE,
  verbose = FALSE
)

Arguments

data	a tibble of airrClone objects, the output of getTrees
node	numeric node in tree (see details)
tree	a phylo tree object containing node
clone	if tree not specified, supply clone ID in data
gaps	add IMGT gaps to output sequences?
translate	Tranlate into amino acids?
rm_x_aa	Remove amino acids translated to X
dot_notation	Represent sites with germline character as "." and ambiguous sites as "?"
verbose	print out extra information?

Value

A data table where each row shows a node/node id, with that node's sequence(s) in the remaining columns with respective locus labels.

See Also

getNodeSeq getAllSeqs dfToFasta

dowser documentation built on Aug. 20, 2026, 5:06 p.m.