Hs: Expected heterozygosity (Hs)

In thibautjombart/adegenet: Exploratory Analysis of Genetic and Genomic Data

Expected heterozygosity (Hs)

Description

This function computes the expected heterozygosity (Hs) within populations of a genpop object. This function is available for codominant markers (@type="codom") only. Hs is commonly used for measuring within population genetic diversity (and as such, it still has sense when computed from haploid data).

Usage

Hs(x, pop = NULL)

Arguments

x	a genind or genpop object.
pop	only used if x is a genind; an optional factor to be used as population; if not provided, pop(x) is used.

Details

Let m(k) be the number of alleles of locus k, with a total of K loci. We note f_i the allele frequency of allele i in a given population. Then, Hs is given for a given population by:

\frac{1}{K} ∑_{k=1}^K (1 - ∑_{i=1}^{m(k)} f_i^2)

Value

a vector of Hs values (one value per population)

Author(s)

Thibaut Jombart [e-mail]

See Also

Hs.test to test differences in Hs between two groups

Examples

## Not run: 
data(nancycats)
Hs(genind2genpop(nancycats))

## End(Not run)

thibautjombart/adegenet documentation built on Feb. 9, 2023, 5:50 p.m.