1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
\name{seg.sites}
\alias{seg.sites}
\title{
Find Segregating Sites in DNA Sequences
}
\usage{
seg.sites(x, strict = FALSE, trailingGapsAsN = TRUE)
}
\arguments{
\item{x}{a matrix or a list which contains the DNA sequences.}
\item{strict}{a logical value; if \code{TRUE}, ambiguities and gaps in
the sequences are not interpreted in the usual way.}
\item{trailingGapsAsN}{a logical value; if \code{TRUE} (the default),
the leading and trailing alignment gaps are considered as unknown
bases (i.e., N).}
}
\description{
This function gives the indices of segregating (polymorphic) sites in
a sample of DNA sequences.
}
\details{
If the sequences are in a list, they must all be of the same length.
If \code{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 \code{strict = TRUE}, all
letters are considered different.
Alignment gaps are considered different from all letters except for
the leading and trailing gaps if \code{trailingGapsAsN = TRUE} (which
is the default).
}
\value{
A numeric (integer) vector giving the indices of the segregating
sites.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{base.freq}}, \code{theta.s}, \code{nuc.div} (last two in \pkg{pegas})
}
\examples{
data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)
}
\keyword{univar}
|
