Heterozygosity.jl

PopGen.jl/src/Heterozygosity.jl

📦 not exported	🔵 exported by PopGen.jl

📦 counthet

counthet(geno::T, allele::Int) where T<:GenoArray
counthet(geno::T, allele::AbstractVector{U}) where T<:GenoArray where U<:Integer

Given a GenoArray, count the number of times allele appears in the heterozygous state.

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📦 counthom

counthom(geno::T, allele::Int) where T<:GenoArray
counthom(geno::T, allele::AbstractVector{U}) where T<:GenoArray where U<:Integer

Given a GenoArray, count the number of times allele appears in the homozygous state.

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📦 _genediversitynei87

_genediversitynei87(het_exp::T, het_obs::T, n::Union{Integer,T}; corr::Bool = true) where T<: AbstractFloat
_genediversitynei87(het_exp::AbstractFloat, het_obs::Missing, n::Union{Integer,AbstractFloat}; corr::Bool = true)
_genediversitynei87(het_exp::Missing, het_obs::AbstractFloat, n::Union{Integer,AbstractFloat}; corr::Bool = true)
_genediversitynei87(het_exp::Missing, het_obs::Missing, n::Union{Integer,AbstractFloat}; corr::Bool = true)

Calculate overall gene diversity with the adjustment/correction given by Nei:

$1-\sum{\bar{p}^2_i + \frac{H_s}{\tilde{n}\times np} - \frac{H_{obs}}{2\tilde{n}\times np}}$

• $\tilde{n}$ is the number of genotypes for a locus for a population
• $np$ is the number of genotypes of a locus across all populations, i.e. $\sum{\tilde{n}}$
• $\bar{p}^2_i$ is the observed homozygosity of a locus for that population
• $H_s$ is the within population gene diversity given by: $H_s = \frac{\tilde{n}}{\tilde{n}-1} \times 1 - (\bar{p}^2_i - \frac{H_{obs}}{2\tilde{n}})$

Nei M. (1987) Molecular Evolutionary Genetics. Columbia University Press

Use corr = false to ignore sample-size correction * n/(n-1)

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📦 _hetero_obs

_hetero_obs(data::T) where T <: GenoArray

Returns observed heterozygosity as a mean of the number of heterozygous genotypes, defined as genotypes returning true for _ishet(). This is numerically feasible because true values are mathematically represented as 1, whereas false are represented as 0.

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📦 _hetero_exp

_hetero_exp(allele_freqs::Vector{T}) where T <: GenoArray

Returns the expected heterozygosity of an array of genotypes, calculated as 1 - sum of the squared allele frequencies.

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🔵 heterozygosity

heterozygosity(data::PopData; by::Union{Symbol,String} = "locus")

Calculate observed and expected heterozygosity in a PopData object. For loci, heterozygosity is calculated in the Nei fashion, such that heterozygosity is calculated as the average over heterozygosity per locus per population.

Modes

• "locus" : heterozygosity per locus (default)
• "sample" : heterozygosity per individual/sample
• "population": heterozygosity per population

Example

heterozygosity(@nancycats, by = "population" )

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📦 _heterozygosity

_heterozygosity(data::PopData, ::Val{:locus})
_heterozygosity(data::PopData, ::Val{:sample})
_heterozygosity(data::PopData, ::Val{:population})

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🔵 samplehet

samplehet(data::PopData, individual::String)

Calculate the observed heterozygosity for an individual in a PopData object.