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\name{range-squeezers}
\alias{range-squeezers}
\alias{ranges}
\alias{rglist}
\alias{rglist,Pairs-method}
\title{Squeeze the ranges out of a range-based object}
\description{
S4 generic functions for squeezing the ranges out of a range-based object.
These are analog to range squeezers \code{\link[GenomicRanges]{granges}}
and \code{\link[GenomicRanges]{grglist}} defined in the \pkg{GenomicRanges}
package, except that \code{ranges} returns the ranges in an \link{IRanges}
object (instead of a \link[GenomicRanges]{GRanges} object for
\code{\link[GenomicRanges]{granges}}), and \code{rglist} returns them in an
\link{IRangesList} object (instead of a \link[GenomicRanges]{GRangesList}
object for \code{\link[GenomicRanges]{grglist}}).
}
\usage{
ranges(x, use.names=TRUE, use.mcols=FALSE, ...)
rglist(x, use.names=TRUE, use.mcols=FALSE, ...)
}
\arguments{
\item{x}{
An object containing ranges e.g. a
\link{IntegerRanges}, \link[GenomicRanges]{GenomicRanges},
\link[SummarizedExperiment]{RangedSummarizedExperiment},
\link[GenomicAlignments]{GAlignments},
\link[GenomicAlignments]{GAlignmentPairs}, or
\link[GenomicAlignments]{GAlignmentsList} object,
or a \link[S4Vectors]{Pairs} object containing ranges.
}
\item{use.names}{
\code{TRUE} (the default) or \code{FALSE}.
Whether or not the names on \code{x} (accessible with \code{names(x)})
should be propagated to the returned object.
}
\item{use.mcols}{
\code{TRUE} or \code{FALSE} (the default).
Whether or not the metadata columns on \code{x} (accessible with
\code{mcols(x)}) should be propagated to the returned object.
}
\item{...}{
Additional arguments, for use in specific methods.
}
}
\details{
Various packages (e.g. \pkg{IRanges}, \pkg{GenomicRanges},
\pkg{SummarizedExperiment}, \pkg{GenomicAlignments}, etc...)
define and document various range squeezing methods for various types
of objects.
Note that these functions can be seen as \emph{object getters} or as
functions performing coercion.
For some objects (e.g. \link[GenomicAlignments]{GAlignments} and
\link[GenomicAlignments]{GAlignmentPairs} objects defined in the
\pkg{GenomicAlignments} package), \code{as(x, "IRanges")} and
\code{as(x, "IRangesList")}, are equivalent to
\code{ranges(x, use.names=TRUE, use.mcols=TRUE)} and
\code{rglist(x, use.names=TRUE, use.mcols=TRUE)}, respectively.
}
\value{
An \link{IRanges} object for \code{ranges}.
An \link{IRangesList} object for \code{rglist}.
If \code{x} is a vector-like object (e.g.
\link[GenomicAlignments]{GAlignments}), the returned object is expected
to be \emph{parallel} to \code{x}, that is, the i-th element in the output
corresponds to the i-th element in the input.
If \code{use.names} is TRUE, then the names on \code{x}
(if any) are propagated to the returned object.
If \code{use.mcols} is TRUE, then the metadata columns on \code{x}
(if any) are propagated to the returned object.
}
\author{H. Pagès}
\seealso{
\itemize{
\item \link{IRanges} and \link{IRangesList} objects.
\item \link[SummarizedExperiment]{RangedSummarizedExperiment} objects
in the \pkg{SummarizedExperiment} packages.
\item \link[GenomicAlignments]{GAlignments},
\link[GenomicAlignments]{GAlignmentPairs},
and \link[GenomicAlignments]{GAlignmentsList} objects in the
\pkg{GenomicAlignments} package.
}
}
\examples{
## See ?GAlignments in the GenomicAlignments package for examples of
## "ranges" and "rglist" methods.
}
\keyword{methods}
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