R: Heterozygosity at a Locus Using Gene Frequencies

heterozygosity {pegas} | R Documentation

## Heterozygosity at a Locus Using Gene Frequencies

### Description

Thes functions compute the mean heterozygosity(ies) from gene frequencies, and return optionally the associated variance(s).

### Usage

    H(x, ...)
    ## S3 method for class 'loci'
    H(x, variance = FALSE, observed = FALSE, ...)
    ## Default S3 method:
    H(x, variance = FALSE, ...)

    heterozygosity(x, variance = FALSE)

### Arguments

`x` | an object of class `"loci"`, or vector or a factor.
`variance` | a logical indicating whether the variance of the estimated heterozygosity should be returned (`TRUE`), the default being `FALSE`.
`observed` | a logical specifying whether to calculate the observed heterozygosity.
`...` | currently unused

### Details

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.

### Value

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

For the `"loci"` method: a numeric matrix with one, two, or three columns with a row for each locus and the values of heterozygosity as columns.

### Author(s)

Emmanuel Paradis

### References

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

### See Also

`theta.s`

### Examples

    data(jaguar)
    H(jaguar, TRUE, TRUE)
    ## use the (old) default method:
    ## convert the data and compute frequencies:
    S <- summary(jaguar)
    ## compute H for all loci:
    sapply(S, function(x) H(x$allele))
    ## ... and its variance
    sapply(S, function(x) H(x$allele, variance = TRUE))

[Package pegas version 0.13 Index]