\name{alphabetByCycle}
\alias{alphabetByCycle}

\title{Summarize alphabet use by cycle (nucleotide position)}
\description{
  This function summarizes nucleotide frequencies per cycle in a
  \code{DNAStringSet} containing DNA strings of uniform width.
}
\usage{
alphabetByCycle(stringSet, alphabet = Biostrings::alphabet(stringSet))
}

\arguments{
  \item{stringSet}{An object of class \code{DNAStringSet}, with uniform width.}
  \item{alphabet}{(Optional) characters represented in the sequence and
    for which frequencies will be tabulated.}
}
\value{
  An integer matrix of counts, with rows corresonding to letters of
  \code{alphabet} and columsn to cycles \code{1:width}.
}
\author{Martin Morgan <mtmorgan@fhcrc.org>}
\seealso{\code{\linkS4class{DNAStringSet}}}
\examples{
example(readSolexaFastQ) # read sequences into 'sq'
alphabetByCycle(sequences(sq))[,2:5] # first five cycles

## specify alpha for scores
alpha <- sapply(33:93, function(i) rawToChar(as.raw(i)))
abc <- alphabetByCycle(scores(sq), alphabet=alpha)
abc[50:61,10:20] ## encoded scores 50:61, cycles 10:20
}
\keyword{manip}