123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354 \name{AlignedRead} \alias{AlignedRead} \title{(Legacy) Construct objects of class "AlignedRead"} \description{ This function constructs objects of \code{\linkS4class{AlignedRead}}. It will often be more convenient to create \code{AlignedRead} objects using parsers such as \code{\link{readAligned}}. } \usage{ AlignedRead(sread, id, quality, chromosome, position, strand, alignQuality, alignData = AlignedDataFrame(nrow = length(sread))) } \arguments{ \item{sread}{An object of class \code{DNAStringSet}, containing the DNA sequences of the short reads.} \item{id}{An object of class \code{BStringSet}, containing the identifiers of the short reads. This object is the same length as \code{sread}.} \item{quality}{An object of class \code{BStringSet}, containing the ASCII-encoded quality scores of the short reads. This object is the same length as \code{sread}.} \item{chromosome}{A \code{factor} describing the particular sequence within a set of target sequences (e.g. chromosomes in a genome assembly) to which each short read aligns.} \item{position}{A \code{integer} vector describing the (base pair) position at which each short read begins its alignment.} \item{strand}{A \code{factor} describing the strand to which the short read aligns.} \item{alignQuality}{A \code{numeric} vector describing the alignment quality.} \item{alignData}{An \code{AlignedDataFrame} with number of rows equal to the length of \code{sread}, containing additional information about alignments.} } \value{ An object of class \code{\linkS4class{AlignedRead}}. } \author{Martin Morgan } \seealso{\code{\linkS4class{AlignedRead}}.} \keyword{manip}