nearest-methods {SummarizedExperiment} | R Documentation

## 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.

### See Also

- RangedSummarizedExperiment objects.

- The nearest man page in the GenomicRanges package where the `nearest` 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)

    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")
    ))

[Package SummarizedExperiment version 1.24.0 Index]