Sites that mutate independently on many branches of the tree, such as 152, 16311 and 16189 in PhyloTree. These are the variants whose effects a tree can find across unrelated lineages.
Usage
recurrentPositions(
min_branches = 10,
types = c("transition", "transversion", "back-mutation"),
mutations = dimoose::phylotree17_mutations
)Arguments
- min_branches
Minimum number of branches (haplogroups) on which the site mutates.
- types
Mutation types to count; by default substitutions and back-mutations. Insertions and deletions are left out, except that a reverted insertion counts as a back-mutation at its insertion site (for example
"5899.1").- mutations
Default phylotree17_mutations.
Examples
head(recurrentPositions())
#> site n_branches
#> 1 152 223
#> 2 16311 147
#> 3 146 132
#> 4 195 130
#> 5 16189 118
#> 6 16129 94