\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)
+base.freq(x, freq = FALSE)
+Ftab(x, y = NULL)
}
\arguments{
\item{x}{a vector, a matrix, or a list which contains the DNA
sequences.}
-}
-\description{
- This function computes the relative frequencies (i.e. percentages) of
- the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
- sample of 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).}
}
\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 stoting the relative frequencies with names
- \code{c("a", "c", "g", "t")}.
+ A numeric vector with names \code{c("a", "c", "g", "t")}, or a four by
+ four matrix with similar dimnames.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\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}