theta.s

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.

See Also

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

Aliases
  • 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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