\name{basecontent}
\alias{basecontent}
\alias{countbases}

\title{Obtain the ATCG content of a gene}
\description{
  WARNING: Both \code{basecontent} and \code{countbases} have been
  deprecated in favor of \code{\link{alphabetFrequency}}.

  These functions accept a character vector representing the nucleotide
  sequences and compute the frequencies of each base (A, C, G, T).
}
\usage{
basecontent(seq)
countbases(seq, dna = TRUE)
}
\arguments{
  \item{seq}{Character vector.}
  \item{dna}{Logical value indicating whether the sequence is DNA
    (\code{TRUE}) or RNA (\code{FALSE})}
}
\details{
  The base frequencies are calculated separately for
  each element of \code{x}.
  The elements of \code{x} can be in upper case, lower case
  or mixed. 
}

\value{
  A matrix with 4 columns and \code{length(x)} rows.  The columns are
  named \code{A}, \code{C}, \code{T}, \code{G}, and the values in each
  column are the counts of the corresponding bases in the elements of
  \code{x}.  When \code{dna=FALSE}, the \code{T} column is replaced with
  a \code{U} column.
}

\author{R. Gentleman, W. Huber, S. Falcon}

\seealso{\code{\link{alphabetFrequency}}, \code{\link{reverseComplement}}}

\examples{
 v<-c("AAACT", "GGGTT", "ggAtT")

 ## Do not use these functions anymore:
 if (interactive()) {
   basecontent(v)
   countbases(v)
 }

 ## But use more efficient alphabetFrequency() instead:
 v <- DNAStringSet(v)
 alphabetFrequency(v, baseOnly=TRUE)

 ## Comparing efficiencies:
 if (interactive()) {
   library(hgu95av2probe)
   system.time(y1 <- countbases(hgu95av2probe$sequence))
   x <- DNAStringSet(hgu95av2probe)
   system.time(y2 <- alphabetFrequency(x, baseOnly=TRUE))
 }
}
\keyword{manip}