nearest-methods: Finding the nearest genomic range/position neighbor

In vjcitn/GenomicRangesGHA: Representation and manipulation of genomic intervals; demo with github actions binary generation

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.

vjcitn/GenomicRangesGHA documentation built on Jan. 18, 2021, 12:39 a.m.