SummarizedExperiment: nearest-methods – R documentation

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nearest-methods

Finding the nearest range neighbor in RangedSummarizedExperiment objects

Description

This man page documents the nearest methods and family (i.e. precede, follow, distance, and distanceToNearest methods) for RangedSummarizedExperiment objects.

Usage

## S4 method for signature 'RangedSummarizedExperiment,ANY'
precede(x, subject, select=c("arbitrary", "all"),
        ignore.strand=FALSE)
## S4 method for signature 'ANY,RangedSummarizedExperiment'
precede(x, subject, select=c("arbitrary", "all"),
        ignore.strand=FALSE)

## S4 method for signature 'RangedSummarizedExperiment,ANY'
follow(x, subject, select=c("arbitrary", "all"),
        ignore.strand=FALSE)
## S4 method for signature 'ANY,RangedSummarizedExperiment'
follow(x, subject, select=c("arbitrary", "all"),
        ignore.strand=FALSE)

## S4 method for signature 'RangedSummarizedExperiment,ANY'
nearest(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
## S4 method for signature 'ANY,RangedSummarizedExperiment'
nearest(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)

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

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

Arguments

`x, subject`	One of these two arguments must be a RangedSummarizedExperiment object.
`select, ignore.strand`	See `?nearest` in the GenomicRanges package.
`y`	For the `distance` methods, one of `x` or `y` must be a RangedSummarizedExperiment object.
`...`	Additional arguments for methods.

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 x, subject, and/or y argument, then it behaves as if rowRanges(x), rowRanges(subject), and/or rowRanges(y) had been passed instead.

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

Value

See ?nearest in the GenomicRanges package.

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)

res <- nearest(rse0, rse1)
res
stopifnot(identical(res, nearest(rowRanges(rse0), rowRanges(rse1))))
stopifnot(identical(res, nearest(rse0, rowRanges(rse1))))
stopifnot(identical(res, nearest(rowRanges(rse0), rse1)))

res <- nearest(rse0)  # missing subject
res
stopifnot(identical(res, nearest(rowRanges(rse0))))

hits <- nearest(rse0, rse1, select="all")
hits
stopifnot(identical(
  hits,
  nearest(rowRanges(rse0), rowRanges(rse1), select="all")
))
stopifnot(identical(
  hits,
  nearest(rse0, rowRanges(rse1), select="all")
))
stopifnot(identical(
  hits,
  nearest(rowRanges(rse0), rse1, select="all")
))

SummarizedExperiment

SummarizedExperiment container

v1.20.0

Artistic-2.0

Authors

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Initial release