SummarizedExperiment (version 1.2.3)

findOverlaps-methods: Finding overlapping ranges in RangedSummarizedExperiment objects

Description

This man page documents the findOverlaps methods for RangedSummarizedExperiment objects.

RangedSummarizedExperiment objects also support countOverlaps, overlapsAny, and subsetByOverlaps thanks to the default methods defined in the IRanges package and to the findOverlaps methods defined in this package and documented below.

Usage

"findOverlaps"(query, subject, maxgap=0L, minoverlap=1L, type=c("any", "start", "end", "within", "equal"), select=c("all", "first", "last", "arbitrary"), ignore.strand=FALSE)
"findOverlaps"(query, subject, maxgap=0L, minoverlap=1L, type=c("any", "start", "end", "within", "equal"), select=c("all", "first", "last", "arbitrary"), ignore.strand=FALSE)

Arguments

query, subject

One of these two arguments must be a RangedSummarizedExperiment object.

maxgap, minoverlap, type

See ?findOverlaps in the GenomicRanges package.

select, ignore.strand

See ?findOverlaps in the GenomicRanges package.

Value

See ?findOverlaps in the GenomicRanges package.

Details

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

More precisely, if any of the above functions is passed a RangedSummarizedExperiment object thru the query and/or subject argument, then it behaves as if rowRanges(query) and/or rowRanges(subject) had been passed instead.

See ?findOverlaps in the GenomicRanges package for the details of how findOverlaps and family operate on GenomicRanges and GRangesList objects.

See Also

• RangedSummarizedExperiment objects.

• The findOverlaps man page in the GenomicRanges package where the findOverlaps family of methods for GenomicRanges and GRangesList objects is 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, 100)

hits <- findOverlaps(rse0, rse1)
hits
stopifnot(identical(hits, findOverlaps(rowRanges(rse0), rowRanges(rse1))))
stopifnot(identical(hits, findOverlaps(rse0, rowRanges(rse1))))
stopifnot(identical(hits, findOverlaps(rowRanges(rse0), rse1)))