pegas (version 0.10)

theta.msat: Population Parameter THETA From Micro-Satellites

Description

This function estimates the population parameter $\theta$ using micro-satellite data with three different estimators.

Usage

theta.msat(x)

Arguments

x

an object of class "loci".

Value

a numeric matrix with loci as rows and the three estimates of $\theta$ as columns.

Details

The data must be micro-satellites, so the allele names must be the repeat counts (see the example).

The three estimators are based on (i) the variance of the number of repeats, (ii) the expected homozygosity (both described in Kimmel et al., 1998), and (iii) the mean allele frequencies (Haasl and Payseur, 2010).

References

Kimmel, M., Chakraborty, R., King, J. P., Bamshad, M., Watkins, W. S. and Jorde, L. B. (1998) Signatures of population expansion in microsatellite repeat data. Genetics, 148, 1921--1930.

Haasl, R. J. and Payseur, B. A. (2010) The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of $\theta$. Molecular Biology and Evolution, 27, 2702--2715.

See Also

theta.h, theta.tree

Examples

# NOT RUN {
data(jaguar)
theta.msat(jaguar)
# }