GitHub

Sample

Moonshine.Sample — Type
struct Sample <: AbstractVector{Sequence}

Contain a sample of haplotypes and informations about them.

Implements the iteration interface and the array interface.

Fields

  • H::Vector{Sequence}: Vector of haplotypes

  • μ::Float64: Unscaled (per-locus) mutation rate

  • ρ::Float64: Unscaled (per-locus) recombination rate

  • Ne::Float64: Effective population size

  • sequence_length::Float64: Sequence length

  • positions::Vector{Float64}: Marker's positions

  • coefs::Tuple{Float64, Float64}: Coefficients for positions' line

Constructors

Info

Random constructor sample sequences via msprime using a binary mutation model.

Sample(H, μ, ρ, Ne, sequence_length, positions, coefs)
Sample(H, μ, ρ, Ne, sequence_length, positions, coefs)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sample.jl:33.

Sample(H; μ, ρ, Ne, sequence_length, positions)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sample.jl:49.

Sample(ts)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sample.jl:64.

Sample(rng, n, μ, ρ, Ne, sequence_length)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sample.jl:102.

where:

  • n: number of sequences
  • rng: random number generator
  • ts: Tree Sequence
source