nearest-methods {GenomicRanges}R Documentation

Finding the nearest genomic range neighbor

Description

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

Usage

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

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

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. If x does not have a match in subject the x is not included in the Hits object.

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

Value

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

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 <vobencha@fhcrc.org>

See Also

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)

  ## -----------------------------------------------------------
  ## 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)

[Package GenomicRanges version 1.12.1 Index]