12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485 \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 } \examples{ fl <- system.file("extdata", package="ShortRead") sp <- SolexaPath(fl) readPrb(sp, "s_1.*_prb.txt") # all tiles to a single file } \keyword{manip}