inter-range-methods {SummarizedExperiment} | R Documentation

## Inter range transformations of a RangedSummarizedExperiment object

### Description

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

### Usage

    ## S4 method for signature 'RangedSummarizedExperiment'
    isDisjoint(x, ignore.strand=FALSE)

    ## S4 method for signature 'RangedSummarizedExperiment'
    disjointBins(x, ignore.strand=FALSE)

### Arguments

`x` | A RangedSummarizedExperiment object.
`ignore.strand` | See `?isDisjoint` in the GenomicRanges 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`:

        f(rowRanges(x), ...)

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

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

### Value

See `?isDisjoint` in the GenomicRanges package.

### See Also

- RangedSummarizedExperiment objects.

- The isDisjoint man page in the GenomicRanges package where inter 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, 99*start(rse0))

    isDisjoint(rse0)  # FALSE
    isDisjoint(rse1)  # TRUE

    bins0 <- disjointBins(rse0)
    bins0
    stopifnot(identical(bins0, disjointBins(rowRanges(rse0))))

    bins1 <- disjointBins(rse1)
    bins1
    stopifnot(all(bins1 == bins1[1]))

[Package SummarizedExperiment version 1.10.1 Index]