pedigrees_all_populate_haplotypes {malan}

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]])