Description Usage Arguments Details Value Author(s) See Also Examples
The nearest
, precede
, follow
, distance
,
nearestKNeighbors
, and distanceToNearest
methods for
GenomicRanges
objects and subclasses.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | ## 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, ...)
|
x |
The query GenomicRanges instance. |
subject |
The subject GenomicRanges instance
within which the nearest neighbors are found. Can be missing,
in which case |
y |
For the |
k |
For the |
select |
Logic for handling ties. By default, all methods
select a single interval (arbitrary for When |
ignore.strand |
A |
... |
Additional arguments for methods. |
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.
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
.
P. Aboyoun and V. Obenchain
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | ## -----------------------------------------------------------
## 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.
|
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