Sibship.jl

PopGenSims.jl/src/Sibship.jl

📦 not exported	🟪 exported by PopGenSims.jl

📦 _cross

_cross(parent1::Vector{Vector{T}}, parent2::Vector{Vector{T}}) where T <: Signed

Simulate a mating cross between two parents, generating one offspring with the same ploidy as parent1. This variant of cross is used internally for simulatekin.

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📦 _parentoffspring

parentoffspring(data::PopData; n::Int, ploidy::Int)

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📦 fullsib

fullsib(data::PopData; n::Int, ploidy::Int)

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📦 halfsib

halfsib(data::PopData; n::Int, ploidy::Int)

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📦 unrelated

unrelated(data::PopData; n::Int, ploidy::Int)

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🟪 simulatekin

simulatekin(data::PopData; fullsib::Int, halfsib::Int, unrelated::Int, parentoffspring::Int, ploidy::Signed)

Simulate mating crosses to generate sample pairs with any combination of the specified relationships, returning a PopData object. The simulations will first generate parents of a given ploidy (inferred or specified) by drawing alleles from a global allele pool derived from the given data (i.e. weighted by their frequencies).

Relationship

Simulated parents will be crossed to generate offspring depending on the relationship:

• fullsib : 2 parents generate 2 full-sibling offspring, return 2 offspring
• halfsib : 3 parents generate 2 half-sibling offspring, returns 2 offspring
• unrelated : returns 2 randomly generated individuals from the global allele pools
• parentoffspring : 2 parents generate 1 offspring, returns 1 offspring and 1 parent

Identifying pairs

The relationship between the newly generated samples can be identified by:

• Sample names will specify their simulation number, relationship, and whether parent or offspring
  • Naming convention: [simulation #][relationship][offspring #]
  • example: sim005fullsib_1 = [simulation 005][full sibling]_[offspring 1]
• Their population name will be that of their relationship (e.g. "fullsib")

Ploidy

If the samples in your PopData are of a single ploidy, then ploidy = 0 (the default) will infer the ploidy and generate parents and offspring according to the ploidy of your data. If you have mixed-ploidy data or wish to generate parents and offspring of a ploidy different than the source PopData you can specify the ploidy with which to simulate parents and offspring. For example, if your PopData is diploid, but you wish to generate triploid or octoploid parents and offspring, you would specify ploidy = 3 or ploidy = 8 repectively.

Odd ploidy

If trying to create offspring with an odd ploidy (3,5, etc.), each parent has a 50% chance of contributing (½ × ploidy) + 1 alleles for all loci to the offspring. In other words, if ploidy = 3, there's a 50% chance parent_1 will give 2 alleles for every locus for that simulated cross.

Example

julia> cats = @nanycats ;

julia> cat_sims = simulatekin(cats, fullsib = 10, halfsib = 50)
PopData{Diploid, 9 Microsatellite loci}
  Samples: 120
  Populations: 2

julia> cat_sims.sampleinfo
120×3 DataFrame
 Row │ name             population  ploidy 
     │ String           String      Int64  
─────┼─────────────────────────────────────
   1 │ sim01_fullsib_1  fullsib          2
   2 │ sim01_fullsib_2  fullsib          2
   3 │ sim02_fullsib_1  fullsib          2
   4 │ sim02_fullsib_2  fullsib          2
   5 │ sim03_fullsib_1  fullsib          2
   6 │ sim03_fullsib_2  fullsib          2
  ⋮  │        ⋮             ⋮         ⋮
 115 │ sim48_halfsib_1  halfsib          2
 116 │ sim48_halfsib_2  halfsib          2
 117 │ sim49_halfsib_1  halfsib          2
 118 │ sim49_halfsib_2  halfsib          2
 119 │ sim50_halfsib_1  halfsib          2
 120 │ sim50_halfsib_2  halfsib          2
                           108 rows omitted