intra-range-methods {SummarizedExperiment} | R Documentation

## Intra range transformations of a RangedSummarizedExperiment object

### Description

This man page documents the intra range transformations that are supported on RangedSummarizedExperiment objects.

### Usage

    ## S4 method for signature 'RangedSummarizedExperiment'
    shift(x, shift=0L, use.names=TRUE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    resize(x, width, fix="start", use.names=TRUE,
           ignore.strand=FALSE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    flank(x, width, start=TRUE, both=FALSE,
          use.names=TRUE, ignore.strand=FALSE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    promoters(x, upstream=2000, downstream=200)

    ## S4 method for signature 'RangedSummarizedExperiment'
    restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
             use.names=TRUE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    trim(x, use.names=TRUE)

### Arguments

`x` | A RangedSummarizedExperiment object.
`shift, use.names` | See `?shift` in the IRanges package.
`start, end, width, fix` | See `?shift` in the IRanges package.
`ignore.strand, both` | See `?shift` in the IRanges package.
`upstream, downstream` | See `?shift` in the IRanges package.
`keep.all.ranges` | See `?shift` in the IRanges package.

### Details

These transformations operate on the `rowRanges` component of the RangedSummarizedExperiment object, which can be a GenomicRanges or GRangesList object.

More precisely, any of the above functions performs the following transformation on RangedSummarizedExperiment object `x`:

        rowRanges(x) <- f(rowRanges(x), ...)

where `f` is the name of the function and `...` any additional arguments passed to it.

See `?shift` in the IRanges package for the details of how these transformations operate on a GenomicRanges or GRangesList object.

### See Also

- RangedSummarizedExperiment objects.

- The shift man page in the IRanges package where intra range transformations of a GenomicRanges or 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 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
    stopifnot(identical(
      rowRanges(se5),
      restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
    ))

[Package SummarizedExperiment version 1.14.1 Index]