checkDivergence - 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.