pegas: theta.h – R documentation

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theta.h

Population Parameter THETA using Homozygosity

Description

This function computes the population parameter THETA using the homozygosity (or mean heterozygosity) from gene frequencies.

Usage

theta.h(x, standard.error = FALSE)

Arguments

`x`	a vector or a factor.
`standard.error`	a logical indicating whether the standard error of the estimated theta 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 standard error is computed with an approximation due to Chakraborty and Weiss (1991).

Value

A numeric vector of length one with the estimated theta (the default), or of length two if the standard error is returned (standard.error = TRUE).

Author(s)

Emmanuel Paradis

References

Zouros, E. (1979) Mutation rates, population sizes and amounts of electrophoretic variation at enzyme loci in natural populations. Genetics, 92, 623–646.

Chakraborty, R. and Weiss, K. M. (1991) Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium. American Journal of Physical Anthropology, 86, 497–506.

Examples

data(jaguar)
## compute frequencies:
S <- summary(jaguar)
## compute THETA for all loci:
sapply(S, function(x) theta.h(x$allele))

pegas

Population and Evolutionary Genetics Analysis System

v1.0

GPL (>= 2)

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)

Initial release

2021-04-08