heterozygosity: Heterozygosity at a Locus Using Gene Frequencies
In dwinter/Pegas: Population and Evolutionary Genetics Analysis System

Description Usage Arguments Details Value Author(s) References See Also Examples

This function computes the mean heterozygosity from gene frequencies, and returns optionally the associated variance.

1 2	heterozygosity(x, variance = FALSE) H(x, variance = FALSE)

`x`	a vector or a factor.
`variance`	a logical indicating whether the variance of the estimated heterozygosity should be returned (`TRUE`), the default being `FALSE`.

The argument x can be either a factor or a vector. If it is a factor, then it is taken to give the individual alleles in the population. If it is a numeric vector, then its values are taken to be the numbers of each allele in the population. If it is a non-numeric vector, it is a coerced as a factor.

The mean heterozygosity is estimated with:

H = n(1 - SUM (FROM i=1 TO k) p_i^2)/(n - 1)

where n is the number of genes in the sample, k is the number of alleles, and p_i is the observed (relative) frequency of the ith allele.

A numeric vector of length one with the estimated mean heterozygosity (the default), or of length two if the variance is returned.

Emmanuel Paradis

Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.

theta.s

require(adegenet)
data(nancycats)
## convert the data and compute frequencies:
S <- summary(as.loci(nancycats))
## compute H for all loci:
sapply(S, function(x) H(x$allele))
## ... and its variance
sapply(S, function(x) H(x$allele, variance = TRUE))