https://github.com/cran/ape
Tip revision: d6915fa45d3617e877036c87482ea56644e8dab9 authored by Emmanuel Paradis on 10 February 2012, 00:00:00 UTC
version 3.0
version 3.0
Tip revision: d6915fa
base.freq.Rd
\name{base.freq}
\alias{base.freq}
\alias{Ftab}
\title{Base frequencies from DNA Sequences}
\description{
\code{base.freq} computes the frequencies (absolute or relative) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.
\code{Ftab} computes the contingency table with the absolute
frequencies of the DNA bases from a pair of sequences.
}
\usage{
base.freq(x, freq = FALSE, all = FALSE)
Ftab(x, y = NULL)
}
\arguments{
\item{x}{a vector, a matrix, or a list which contains the DNA
sequences.}
\item{y}{a vector with a single DNA sequence.}
\item{freq}{a logical specifying whether to return the proportions
(the default) or the absolute frequencies (counts).}
\item{all}{a logical; by default only the counts of A, C, G, and T are
returned. If \code{all = TRUE}, all counts of bases, ambiguous codes,
missing data, and alignment gaps are returned.}
}
\details{
The base frequencies are computed over all sequences in the
sample. All missing or unknown sites are discarded from the
computations.
For \code{Ftab}, if the argument \code{y} is given then both \code{x}
and \code{y} are coerced as vectors and must be of equal length. If
\code{y} is not given, \code{x} must be a matrix or a list and only
the two first sequences are used.
}
\value{
A numeric vector with names \code{c("a", "c", "g", "t")}, or a four by
four matrix with similar dimnames.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{GC.content}}, \code{\link{seg.sites}},
\code{\link{nuc.div}}, \code{\link{DNAbin}}
}
\examples{
data(woodmouse)
base.freq(woodmouse)
base.freq(woodmouse, TRUE)
Ftab(woodmouse)
Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
Ftab(woodmouse[14:15, ]) # between the last two
}
\keyword{univar}
\keyword{manip}