pedigrees_all_populate_haplotypes: Populate haplotypes in pedigrees (0-founder/unbounded).

In malan: MAle Lineage ANalysis

Populate haplotypes in pedigrees (0-founder/unbounded).

Description

Populate haplotypes from founder and down in all pedigrees. Note, that haplotypes are unbounded and that all founders get haplotype rep(0L, loci).

Usage

pedigrees_all_populate_haplotypes(
  pedigrees,
  loci,
  mutation_rates,
  prob_two_step = 0,
  prob_genealogical_error = 0,
  progress = TRUE
)

Arguments

pedigrees	Pedigree list in which to populate haplotypes
loci	Number of loci
mutation_rates	Vector with mutation rates, length loci
prob_two_step	Given a mutation happens, this is the probability that the mutation is a two-step mutation
prob_genealogical_error	Probability that a genealogical error happens: if so, give individual haplotype rep(0L, loci) instead of father's
progress	Show progress

Details

Note, that pedigrees must first have been inferred by build_pedigrees().

See Also

pedigrees_all_populate_haplotypes_custom_founders() and pedigrees_all_populate_haplotypes_ladder_bounded().

Examples

sim <- sample_geneology(100, 10)
peds <- build_pedigrees(sim$population)
pedigrees_all_populate_haplotypes(peds, 2, c(1, 1))
get_haplotype(sim$end_generation_individuals[[1]])

malan documentation built on July 4, 2024, 9:09 a.m.