\name{intra-range-methods}
 
 \alias{intra-range-methods}
 
 \alias{shift}
 \alias{shift,RangedSummarizedExperiment-method}
 
 \alias{narrow}
 \alias{narrow,RangedSummarizedExperiment-method}
 
 \alias{resize}
 \alias{resize,RangedSummarizedExperiment-method}
 
 \alias{flank}
 \alias{flank,RangedSummarizedExperiment-method}
 
 \alias{promoters}

 \alias{terminators}

 \alias{promoters,RangedSummarizedExperiment-method}

 \alias{terminators,RangedSummarizedExperiment-method}

 
 \alias{restrict}
 \alias{restrict,RangedSummarizedExperiment-method}
 
 \alias{trim,RangedSummarizedExperiment-method}
 
 
 \title{Intra range transformations of a RangedSummarizedExperiment object}
 
 \description{

   This man page documents the \emph{intra range transformations} that are
   supported on \link{RangedSummarizedExperiment} objects.

 }
 
 \usage{
 \S4method{shift}{RangedSummarizedExperiment}(x, shift=0L, use.names=TRUE)
 
 \S4method{narrow}{RangedSummarizedExperiment}(x, start=NA, end=NA, width=NA, use.names=TRUE)
 
 \S4method{resize}{RangedSummarizedExperiment}(x, width, fix="start", use.names=TRUE,
        ignore.strand=FALSE)
 
 \S4method{flank}{RangedSummarizedExperiment}(x, width, start=TRUE, both=FALSE,
       use.names=TRUE, ignore.strand=FALSE)
 
 \S4method{promoters}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)

 \S4method{terminators}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)

 
 \S4method{restrict}{RangedSummarizedExperiment}(x, start=NA, end=NA, keep.all.ranges=FALSE,
          use.names=TRUE)
 
 \S4method{trim}{RangedSummarizedExperiment}(x, use.names=TRUE)
 }
 
 \arguments{
   \item{x}{
     A \link{RangedSummarizedExperiment} object.
   }

   \item{shift, use.names, start, end, width, fix, ignore.strand, both,
         upstream, downstream, keep.all.ranges}{
     See \code{?GenomicRanges::\link[GenomicRanges]{shift}} in the
     \pkg{GenomicRanges} package.

   }
 }
 
 \details{

   These transformations operate on the \code{rowRanges} component of the
   \link{RangedSummarizedExperiment} object, which can be a
   \link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
   object.
 
   More precisely, any of the above functions performs the following
   transformation on \link{RangedSummarizedExperiment} object \code{x}:
 \preformatted{    rowRanges(x) <- f(rowRanges(x), ...)

 }
   where \code{f} is the name of the function and \code{...} any additional

   arguments passed to it.

   See \code{?GenomicRanges::\link[GenomicRanges]{shift}} in the
   \pkg{GenomicRanges} package for the details of how these transformations
   operate on a \link[GenomicRanges]{GenomicRanges} or
   \link[GenomicRanges]{GRangesList}

   object.

 }
 
 \seealso{
   \itemize{
     \item \link{RangedSummarizedExperiment} objects.

     \item The \code{\link[GenomicRanges]{shift}} man page in the
           \pkg{GenomicRanges} package where \emph{intra range transformations}

           of a \link[GenomicRanges]{GenomicRanges} or
           \link[GenomicRanges]{GRangesList} object are documented.

   }
 }
 
 \examples{
 nrows <- 20; ncols <- 6
 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
 rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
                      IRanges(sample(1000L, 20), width=100),
                      strand=Rle(c("+", "-"), c(12, 8)))
 colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                      row.names=LETTERS[1:6])

 rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
                              rowRanges=rowRanges, colData=colData)

 rse1 <- shift(rse0, 1)

 stopifnot(identical(

   rowRanges(rse1),
   shift(rowRanges(rse0), 1)

 ))
 

 se2 <- narrow(rse0, start=10, end=-15)

 stopifnot(identical(
   rowRanges(se2),

   narrow(rowRanges(rse0), start=10, end=-15)

 ))
 

 se3 <- resize(rse0, width=75)

 stopifnot(identical(
   rowRanges(se3),

   resize(rowRanges(rse0), width=75)

 ))
 

 se4 <- flank(rse0, width=20)

 stopifnot(identical(
   rowRanges(se4),

   flank(rowRanges(rse0), width=20)

 ))
 

 se5 <- promoters(rse0, upstream=85, downstream=50)

 stopifnot(identical(
   rowRanges(se5),

   promoters(rowRanges(rse0), upstream=85, downstream=50)
 ))
 
 se6 <- terminators(rse0, upstream=85, downstream=50)
 stopifnot(identical(
   rowRanges(se6),
   terminators(rowRanges(rse0), upstream=85, downstream=50)
 ))
 
 se7 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
 stopifnot(identical(
   rowRanges(se7),

   restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)

 ))
 }
 
 \keyword{methods}
 \keyword{utilities}