pedigrees_all_populate_haplotypes_custom_founders | R Documentation |
Populate haplotypes from founder and down in all pedigrees.
Note, that haplotypes are unbounded.
All founders get a haplotype from calling the user
provided function get_founder_haplotype()
.
pedigrees_all_populate_haplotypes_custom_founders(
pedigrees,
mutation_rates,
get_founder_haplotype = NULL,
prob_two_step = 0,
prob_genealogical_error = 0,
progress = TRUE
)
pedigrees |
Pedigree list in which to populate haplotypes |
mutation_rates |
Vector with mutation rates |
get_founder_haplotype |
Function taking no arguments returning a haplotype of |
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 |
progress |
Show progress |
Note, that pedigrees must first have been inferred by build_pedigrees()
.
pedigrees_all_populate_haplotypes()
and
pedigrees_all_populate_haplotypes_ladder_bounded()
.
sim <- sample_geneology(100, 10)
peds <- build_pedigrees(sim$population)
pedigrees_all_populate_haplotypes_custom_founders(
peds, c(1, 1), function(x) c(10, 10))
get_haplotype(sim$end_generation_individuals[[1]])
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