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\name{setops-methods}
\alias{setops-methods}
\alias{pintersect,GAlignments,GRanges-method}
\alias{pintersect,GRanges,GAlignments-method}
\title{Set operations on GAlignments objects}
\description{
Performs set operations on \link{GAlignments} objects.
}
\usage{
\S4method{pintersect}{GAlignments,GRanges}(x, y, ...)
\S4method{pintersect}{GRanges,GAlignments}(x, y, ...)
}
\arguments{
\item{x, y}{
A \link{GAlignments} object and a \link[GenomicRanges]{GRanges} object.
They must have the same length.
}
\item{...}{
Further arguments to be passed to or from other methods.
}
}
\value{
A \link{GAlignments} object \emph{parallel} to (i.e. same length as)
\code{x} and \code{y}.
}
\seealso{
\itemize{
\item The \link{GAlignments} class.
\item The \link[GenomicRanges]{setops-methods} man page in the
\pkg{GenomicRanges} package.
}
}
\examples{
## Parallel intersection of a GAlignments and a GRanges object:
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools")
gal <- readGAlignments(bamfile)
pintersect(gal, shift(as(gal, "GRanges"), 6L))
}
\keyword{methods}
\keyword{utilities}
|
