R: Population Parameter THETA using Segregating Sites

theta.s {pegas} | R Documentation

## Population Parameter THETA using Segregating Sites

### Description

This function computes the population parameter THETA using the number of segregating sites s in a sample of n DNA sequences.

### Usage

    theta.s(x, ...)
    ## S3 method for class 'DNAbin'
    theta.s(x, variance = FALSE, ...)
    ## Default S3 method:
    theta.s(x, n, variance = FALSE, ...)

### Arguments

`x` | a numeric giving the number of segregating sites.
`n` | a numeric giving the number of sequences.
`variance` | a logical indicating whether the variance of the estimated THETA should be returned (`TRUE`), the default being `FALSE`.
`...` | arguments passed to methods.

### Value

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

### Note

The number of segregating sites needs to be computed beforehand, for instance with the function `seg.sites` (see example below).

### Author(s)

Emmanuel Paradis

### References

Watterson, G. A. (1975) On the number of segragating sites in genetical models without recombination. Theoretical Population Biology, 7, 256–276.

Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.

### See Also

`theta.h`, `theta.k`, `seg.sites`, `nuc.div`, `theta.tree`

### Examples

    data(woodmouse)
    theta.s(woodmouse)
    theta.s(woodmouse, variance = TRUE)
    ## using the default:
    s <- length(seg.sites(woodmouse))
    n <- nrow(woodmouse)
    theta.s(s, n)

[Package pegas version 0.13 Index]