heterozygosity

0th

Percentile

Heterozygosity at a Locus Using Gene Frequencies

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

Keywords
manip, univar
Usage
heterozygosity(x, variance = FALSE)
H(x, variance = FALSE)
Arguments
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.
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:

$$\hat{H} = \frac{n}{n-1} \left(1 - \sum_{i=1}^k p_i^2 \right)$$

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 allele $i$.

Value

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

References

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

See Also

theta.s

Aliases
  • heterozygosity
  • H
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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