seg.sites {ape}R Documentation

Find Segregating Sites in DNA Sequences

Description

This function gives the indices of segregating (polymorphic) sites in a sample of DNA sequences.

Usage

seg.sites(x, strict = FALSE, trailingGapsAsN = TRUE)

Arguments

x

a matrix or a list which contains the DNA sequences.

strict

a logical value; if TRUE, ambiguities and gaps in the sequences are not interpreted in the usual way.

trailingGapsAsN

a logical value; if TRUE (the default), the leading and trailing alignment gaps are considered as unknown bases (i.e., N).

Details

If the sequences are in a list, they must all be of the same length.

If strict = FALSE (the default), the following rule is used to determine if a site is polymorphic or not in the presence of ambiguous bases: ‘A’ and ‘R’ are not interpreted as different, ‘A’ and ‘Y’ are interpreted as different, and ‘N’ and any other base (ambiguous or not) are interpreted as not different. If strict = TRUE, all letters are considered different.

Alignment gaps are considered different from all letters except for the leading and trailing gaps if trailingGapsAsN = TRUE (which is the default).

Value

A numeric (integer) vector giving the indices of the segregating sites.

Author(s)

Emmanuel Paradis

See Also

base.freq, theta.s, nuc.div (last two in pegas)

Examples

data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)

[Package ape version 5.5 Index]