R: Finding the nearest genomic range neighbor

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("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'
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`.
`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 IRanges, ?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.
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 IRanges for 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>

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)

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

[Package GenomicRanges version 1.30.1 Index]