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\name{readPrb}
\alias{readPrb}
\alias{readPrb,character-method}
\title{(Legacy) Read Solexa prb files as fastq-style quality scores}
\description{
\code{readPrb} reads all \code{_prb.txt} files in a directory into a
single object. Most methods (see details) do this by identifying the
maximum base call quality for each cycle and read, and representing
this as an ASCII-encoded character string.
}
\usage{
readPrb(dirPath, pattern = character(0), ...)
}
\arguments{
\item{dirPath}{Directory path or other object (e.g.,
\code{\linkS4class{SolexaPath}} for which methods are defined.}
\item{pattern}{Regular expression matching names of \code{_prb} files
to be summarized.}
\item{\dots}{Additional arguments, unused.}
}
\details{
The \code{readPrb,character-method} contains an argument \code{as}
that determines the value of the returned object, as follows.
\describe{
\item{\code{as="SolexaEncoding"}}{
The ASCII encoding of the maximum per cycle and read quality score
is encoded using Solexa conventions.
}
\item{\code{as="FastqEncoding"}}{
The ASCII encoding of the maximum per cycle and read quality score
is encoded using Fastq conventions, i.e., \code{!} has value 0.
}
\item{\code{as="IntegerEncoding"}}{
The maximum per cycle and read quality score is returned as a in
integer value. Values are collated into a matrix with number of
rows equal to number of reads, and number of columns equal to
number of cycles.
}
\item{\code{as="array"}}{
The quality scores are \emph{not} summarized; the return value is
an integer array with dimensions corresponding to reads,
nucleotides, and cycles.
}
}
}
\value{
An object of class \code{\linkS4class{QualityScore}}, or an integer matrix.
}
\author{Martin Morgan <mtmorgan@fhcrc.org>}
\examples{
fl <- system.file("extdata", package="ShortRead")
sp <- SolexaPath(fl)
readPrb(sp, "s_1.*_prb.txt") # all tiles to a single file
}
\keyword{manip}
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