nearest-methods {GenomicRanges} | R Documentation

## Finding the nearest genomic range/position neighbor

### Description

The `nearest`, `precede`, `follow`, `distance`, `nearestKNeighbors`, and `distanceToNearest` methods for `GenomicRanges` objects and subclasses.

### Usage

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    precede(x, subject,
        select=c("first", "all"), ignore.strand=FALSE)
    ## S4 method for signature 'GenomicRanges,missing'
    precede(x, subject,
        select=c("first", "all"), ignore.strand=FALSE)

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    follow(x, subject,
        select=c("last", "all"), ignore.strand=FALSE)
    ## S4 method for signature 'GenomicRanges,missing'
    follow(x, subject,
        select=c("last", "all"), ignore.strand=FALSE)

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

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    nearestKNeighbors(x, subject, k=1L,
        select=c("arbitrary", "all"), ignore.strand=FALSE)
    ## S4 method for signature 'GenomicRanges,missing'
    nearestKNeighbors(x, subject, k=1L,
        select=c("arbitrary", "all"), ignore.strand=FALSE)

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

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

### Arguments

`x` | The query GenomicRanges instance.
`subject` | The subject GenomicRanges instance within which the nearest neighbors are found. Can be missing, in which case `x` is also the subject.
`y` | For the `distance` method, a `GRanges` instance. Cannot be missing. If `x` and `y` are not the same length, the shortest will be recycled to match the length of the longest.
`k` | For the `nearestKNeighbors` method, an `integer` declaring how many nearest neighbors to find.
`select` | Logic for handling ties. By default, all methods select a single interval (arbitrary for `nearest`, the first by order in `subject` for `precede`, and the last for `follow`). When `select="all"` a Hits object is returned with all matches for `x`.
`ignore.strand` | A `logical` indicating if the strand of the input ranges should be ignored. When `TRUE`, strand is set to `'+'`.
`...` | Additional arguments for methods.

### Details

- nearest: Performs conventional nearest neighbor finding. Returns an integer vector containing the index of the nearest neighbor range in `subject` for each range in `x`. If there is no nearest neighbor `NA` is returned. For details of the algorithm see the man page in the IRanges package (`?nearest`).

- precede: For each range in `x`, `precede` returns the index of the range in `subject` that is directly preceded by the range in `x`. Overlapping ranges are excluded. `NA` is returned when there are no qualifying ranges in `subject`.

- follow: The opposite of `precede`, `follow` returns the index of the range in `subject` that is directly followed by the range in `x`. Overlapping ranges are excluded. `NA` is returned when there are no qualifying ranges in `subject`.

- nearestKNeighbors: Performs conventional k-nearest neighbor finding. Returns an IntegerList containing the index of the k-nearest neighbors in `subject` for each range in `x`. If there is no nearest neighbor `NA` is returned. If `select="all"` is specified, ties will be included in the resulting IntegerList.

- Orientation and strand for `precede` and `follow`: Orientation is 5' to 3', consistent with the direction of translation. Because positional numbering along a chromosome is from left to right and transcription takes place from 5' to 3', `precede` and `follow` can appear to have ‘opposite’ behavior on the `+` and `-` strand. Using positions 5 and 6 as an example, 5 precedes 6 on the `+` strand but follows 6 on the `-` strand.

  The table below outlines the orientation when ranges on different strands are compared. In general, a feature on `*` is considered to belong to both strands. The single exception is when both `x` and `subject` are `*` in which case both are treated as `+`.

             x  |  subject  |  orientation
           -----+-----------+----------------
      a)     +  |  +        |  --->
      b)     +  |  -        |  NA
      c)     +  |  *        |  --->
      d)     -  |  +        |  NA
      e)     -  |  -        |  <---
      f)     -  |  *        |  <---
      g)     *  |  +        |  --->
      h)     *  |  -        |  <---
      i)     *  |  *        |  --->  (the only situation where * arbitrarily means +)

- distanceToNearest: Returns the distance for each range in `x` to its nearest neighbor in the `subject`.

- distance: Returns the distance for each range in `x` to the range in `y`. The behavior of `distance` has changed in Bioconductor 2.12. See the man page `?distance` in the IRanges package for details.

### Value

For `nearest`, `precede` and `follow`, an integer vector of indices in `subject`, or a Hits if `select="all"`.

For `nearestKNeighbors`, an IntegerList of vertices in `subject`.

For `distanceToNearest`, a Hits object with a column for the `query` index (queryHits), `subject` index (subjectHits) and the `distance` between the pair.

For `distance`, an integer vector of distances between the ranges in `x` and `y`.

### Author(s)

P. Aboyoun and V. Obenchain

### See Also

- The GenomicRanges and GRanges classes.

- The IntegerRanges class in the IRanges package.

- The Hits class in the S4Vectors package.

- The nearest-methods man page in the IRanges package.

- findOverlaps-methods for finding just the overlapping ranges.

- The nearest-methods man page in the GenomicFeatures package.

### Examples

    ## -----------------------------------------------------------
    ## precede() and follow()
    ## -----------------------------------------------------------
    query <- GRanges("A", IRanges(c(5, 20), width=1), strand="+")
    subject <- GRanges("A", IRanges(rep(c(10, 15), 2), width=1),
                            strand=c("+", "+", "-", "-"))
    precede(query, subject)
    follow(query, subject)

    strand(query) <- "-"
    precede(query, subject)
    follow(query, subject)

    ## ties choose first in order
    query <- GRanges("A", IRanges(10, width=1), c("+", "-", "*"))
    subject <- GRanges("A", IRanges(c(5, 5, 5, 15, 15, 15), width=1),
                            rep(c("+", "-", "*"), 2))
    precede(query, subject)
    precede(query, rev(subject))

    ## ignore.strand=TRUE treats all ranges as '+'
    precede(query[1], subject[4:6], select="all", ignore.strand=FALSE)
    precede(query[1], subject[4:6], select="all", ignore.strand=TRUE)

    ## -----------------------------------------------------------
    ## nearest()
    ## -----------------------------------------------------------
    ## When multiple ranges overlap an "arbitrary" range is chosen
    query <- GRanges("A", IRanges(5, 15))
    subject <- GRanges("A", IRanges(c(1, 15), c(5, 19)))
    nearest(query, subject)

    ## select="all" returns all hits
    nearest(query, subject, select="all")

    ## Ranges in 'x' will self-select when 'subject' is present
    query <- GRanges("A", IRanges(c(1, 10), width=5))
    nearest(query, query)

    ## Ranges in 'x' will not self-select when 'subject' is missing
    nearest(query)

    ## -----------------------------------------------------------
    ## nearestKNeighbors()
    ## -----------------------------------------------------------
    ## Without an argument, k defaults to 1
    query <- GRanges("A", IRanges(c(2, 5), c(8, 15)))
    subject <- GRanges("A", IRanges(c(1, 4, 10, 15), c(5, 7, 12, 19)))
    nearestKNeighbors(query, subject)

    ## Return multiple neighbors with k > 1
    nearestKNeighbors(query, subject, k=3)

    ## select="all" returns all hits
    nearestKNeighbors(query, subject, select="all")

    ## -----------------------------------------------------------
    ## distance(), distanceToNearest()
    ## -----------------------------------------------------------
    ## Adjacent, overlap, separated by 1
    query <- GRanges("A", IRanges(c(1, 2, 10), c(5, 8, 11)))
    subject <- GRanges("A", IRanges(c(6, 5, 13), c(10, 10, 15)))
    distance(query, subject)

    ## recycling
    distance(query[1], subject)

    ## zero-width ranges
    zw <- GRanges("A", IRanges(4,3))
    stopifnot(distance(zw, GRanges("A", IRanges(3,4))) == 0L)
    sapply(-3:3, function(i)
        distance(shift(zw, i), GRanges("A", IRanges(4,3))))

    query <- GRanges(c("A", "B"), IRanges(c(1, 5), width=1))
    distanceToNearest(query, subject)

    ## distance() with GRanges and TxDb see the
    ## ?'distance,GenomicRanges,TxDb-method' man
    ## page in the GenomicFeatures package.

[Package GenomicRanges version 1.46.1 Index]