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Sequence

Sequences

Moonshine.Sequence — Type
struct Sequence

Sequence of biallelic genetic markers (haplotype).

Implement the iteration interface as well as standard bitwise operations.

Info

Random constructors sample marker's states via Random.bitrand.

Fields

  • data::BitVector

Constructors

Sequence(data)
Sequence(data)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sequence.jl:48.

Sequence()

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sequence.jl:187.

Sequence(undef, n)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sequence.jl:189.

Sequence(rng, n)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sequence.jl:191.

Sequence(rng, minlength, maxlength)

defined at /home/runner/work/Moonshine.jl/Moonshine.jl/src/Sequence.jl:193.

where:

  • n: number of markers
  • rng: random number generator
  • minLength, maxLength: bounds for sequence length
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Moonshine.idxinchunk — Function
idxinchunk(n, x)
idxinchunk(::Type{Sequence}, x)
idxinchunk(::Sequence, x)

Index of marker x in its associated chunk.

See also chunkidx.

–Internal–

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Moonshine.chunkidx — Function
chunkidx(n, x)
chunkidx(::Type{Sequence}, x)
chunkidx(::Sequence, x)

Index of the chunk associated with marker x.

See also idxinchunk.

–Internal–

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Moonshine.plot_sequence — Function
plot_sequence(h; nbins, height, kwargs...)

Unicode-graphic representation of an haplotype.

Arguments

  • nbins (clamp(length(h), 1, 69)): number of bins
  • ̀height (7): number of rows
  • kwargs: arguments passed directly to UnicodePlots.heatmap
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Distances

Moonshine.Distance — Type
abstract type Distance{T}

Distance between two Sequences.

Implementation

The only required method for a distance D<:Distance to be usable for tree contruction is

distance(::D{T}, ::Sequence, ::Sequence) where T

It is also useful to implement a default constructor. For example, if D is a discrete distance,

D() = D{Int}()
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Moonshine.LeftM — Type
struct LeftM{T} <: Distance{T}

Left marker distance.

This is only the discrete metric for the leftmost marker. Technically not a metric for haplotypes, but widely used.

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