pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists: Information about matching individuals

In malan: MAle Lineage ANalysis

Description

Gives information about all individuals in pedigree that matches an individual. Just as count_haplotype_occurrences_individuals() counts the number of occurrences amongst a list of individuals, this gives detailed information about matching individuals in the pedigree, e.g. meiotic distances and maximum L1 distance on the path as some of these matches may have (back)mutations between in between them (but often this will be 0).

Usage

pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists(
  suspect,
  generation_upper_bound_in_result = -1L
)

Arguments

suspect	Individual that others must match the profile of.
generation_upper_bound_in_result	Only consider matches in generation 0, 1, ... generation_upper_bound_in_result. -1 means disabled, consider all generations. End generation is generation 0. Second last generation is 1. And so on.

Value

Matrix with information about matching individuals. Columns in order: meioses (meiotic distance to suspect), max_L1 (on the path between the matching individual and suspect, what is the maximum L1 distance between the suspect's profile and the profiles of the individuals on the path), pid (pid of matching individual)

See Also

count_haplotype_occurrences_individuals().

malan documentation built on July 2, 2020, 3:01 a.m.