# theta.s

From ape v2.1-1
0th

Percentile

##### Population Parameter THETA using Segregating Sites in DNA Sequences

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

Keywords
manip, univar
##### Usage
theta.s(s, n, variance = FALSE)
##### Arguments
s
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.
##### 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).

##### References

Watterson, G. (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.

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

• theta.s
##### Examples
data(woodmouse)
y <- seg.sites(woodmouse)
s <- length(y)
n <- length(woodmouse)
theta.s(s, n)
theta.s(s, n, variance = TRUE)
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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