SummarizedExperiment (version 1.2.3)

inter-range-methods: Inter range transformations of a RangedSummarizedExperiment object

Description

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

Usage

"isDisjoint"(x, ignore.strand=FALSE)
"disjointBins"(x, ignore.strand=FALSE)

Arguments

x

A RangedSummarizedExperiment object.

ignore.strand

See ?isDisjoint in the GenomicRanges package.

Value

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.

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]))