Which mutations each haplogroup carries

Follows every haplogroup's path from the root of the tree and records, for each requested site, whether the haplogroup's haplotype differs from the root (RSRS) there. Back-mutations are applied as Haplogrep defines them (they undo the latest change at that site), so a site gained and later reverted on a lineage is not carried below the reversion. Insertions are tracked as their own sites ("573.X", "2491.1"), separate from substitutions at the same position; a deletion counts as carried.

Usage

haplotypeMatrix(
  haplogroups,
  sites = NULL,
  tree = dimoose::phylotree17,
  mutations = dimoose::phylotree17_mutations
)

Arguments

haplogroups

Haplogroup names, one per row of the result; repeats are allowed (e.g. one per sample).

sites

Sites to report: positions as character ("16311") or insertion sites ("573.X"). Defaults to the sites of recurrentPositions().

tree, mutations

The tree and its mutations; default phylotree17 and phylotree17_mutations. tree needs haplogroup, parent and depth; mutations needs haplogroup, notation, position, type, ancestral and derived.

Value

An integer matrix of 0/1, one row per entry of haplogroups (row names are the haplogroups) and one column per site.

See also

recurrentPositions(), macroHaplogroup(), simulateExpression()

Examples

haplotypeMatrix(c("H2a2a1", "U5b", "L0a1b"), sites = c("152", "16311", "16278"))
#>        152 16311 16278
#> H2a2a1   1     1     1
#> U5b      1     1     1
#> L0a1b    0     0     0