checkDivergence: Compare divergence along a tree in terms of mutations (sum of...

In dowser: B Cell Receptor Phylogenetics Toolkit

Compare divergence along a tree in terms of mutations (sum of branches) for each tip and reconstructed internal node to its Hamming distance from the germline. Divergence should never be less than Hamming distance. A threshold of -1 is used to represent 1 full mutation difference. The function will throw a warning if any trees cross this threshold

Description

Compare divergence along a tree in terms of mutations (sum of branches) for each tip and reconstructed internal node to its Hamming distance from the germline. Divergence should never be less than Hamming distance. A threshold of -1 is used to represent 1 full mutation difference. The function will throw a warning if any trees cross this threshold

Usage

checkDivergence(
  clones,
  threshold = -1,
  verbose = TRUE,
  germline = "Germline",
  data_type = "DNA"
)

Arguments

clones	a tibble of clones and trees, output from getTrees
threshold	Minimum allowed value of divergence minus Hamming distance
verbose	Print whether all trees passed
germline	ID of the tree's predicted germline sequence
data_type	The type of data being used. Either "DNA" (default) or "AA"

Value

tibble showing the clone_id, sequence_id, as well as tree-based divergence, hamming distance, and difference between the two.

dowser documentation built on Nov. 5, 2025, 6:36 p.m.