findOverlaps-methods: Finding overlapping genomic ranges
In Bioconductor/GenomicRanges: Representation and manipulation of genomic intervals
findOverlaps-methods R Documentation
Finding overlapping genomic ranges
Description
Various methods for finding/counting overlaps between objects containing
genomic ranges. This man page describes the methods that operate on
GenomicRanges and GRangesList objects.
NOTE: The findOverlaps generic function
and methods for IntegerRanges and
IntegerRangesList objects are defined and
documented in the IRanges package.
The methods for GAlignments,
GAlignmentPairs, and
GAlignmentsList objects are defined and
documented in the GenomicAlignments package.
GenomicRanges and GRangesList objects also support
countOverlaps, overlapsAny, and subsetByOverlaps
thanks to the default methods defined in the IRanges package and
to the findOverlaps and countOverlaps methods defined in
this package and documented below.
Usage
## S4 method for signature 'GenomicRanges,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GRangesList,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GRangesList'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GRangesList,GRangesList'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GenomicRanges'
countOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
ignore.strand=FALSE)
Arguments
query, subject
A GRanges or GRangesList object.
maxgap, minoverlap, type
See ?findOverlaps in the IRanges package
for a description of these arguments.
IMPORTANT NOTE about how minoverlap is interpreted when
query or subject is a GRangesList object:
In this case, the total number of overlapping positions between
a given element in query and a given element in subject
is taken into account. For example, if query is a GRanges
object, and subject a GRangesList object, then
findOverlaps() will report an overlap between query[i]
(a single range) and subject[[j]] (multiple ranges) only if
the total number of positions in subject[[j]] that overlap with
query[i] is equal to minoverlap or greater. In other words,
the full overlap across all the ranges in subject[[j]] is looked
at. See the Examples section below for an example illustrating this.
select
When select is "all" (the default), the results are
returned as a Hits object.
Otherwise the returned value is an integer vector parallel to query
(i.e. same length) containing the first, last, or arbitrary overlapping
interval in subject, with NA indicating intervals that did
not overlap any intervals in subject.
ignore.strand
When set to TRUE, the strand information is ignored in the
overlap calculations.
Details
When the query and the subject are GRanges or
GRangesList objects, findOverlaps uses the triplet
(sequence name, range, strand) to determine which features (see
paragraph below for the definition of feature) from the query
overlap which features in the subject, where a strand value
of "*" is treated as occurring on both the "+" and
"-" strand.
An overlap is recorded when a feature in the query and a feature
in the subject have the same sequence name, have a compatible
pairing of strands (e.g. "+"/"+", "-"/"-",
"*"/"+", "*"/"-", etc.), and satisfy the
interval overlap requirements.
In the context of findOverlaps, a feature is a collection of
ranges that are treated as a single entity. For GRanges objects,
a feature is a single range; while for GRangesList objects,
a feature is a list element containing a set of ranges. In the results,
the features are referred to by number, which run from 1 to
length(query)/length(subject).
For type="equal" with GRangesList objects, query[[i]]
matches subject[[j]] iff for each range in query[[i]]
there is an identical range in subject[[j]], and vice versa.
Value
For findOverlaps: either a Hits object when
select="all" or an integer vector otherwise.
For countOverlaps: an integer vector containing the tabulated
query overlap hits.
Author(s)
P. Aboyoun, S. Falcon, M. Lawrence, and H. Pagès
See Also
The Hits class in the S4Vectors package
for representing a set of hits between 2 vector-like objects.
The findOverlaps generic function defined
in the IRanges package.
The GNCList constructor and class for preprocessing and
representing a GenomicRanges or object as a data structure
based on Nested Containment Lists.
The GRanges and GRangesList classes.
Examples
## ---------------------------------------------------------------------
## BASIC EXAMPLES
## ---------------------------------------------------------------------
## GRanges object:
gr <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
score=1:10,
GC=seq(1, 0, length=10)
)
gr
## GRangesList object:
gr1 <- GRanges(seqnames="chr2", ranges=IRanges(4:3, 6),
strand="+", score=5:4, GC=0.45)
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width=3),
strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(c(1, 4), c(3, 9)),
strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
grl <- GRangesList("gr1"=gr1, "gr2"=gr2, "gr3"=gr3)
## Overlapping two GRanges objects:
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
countOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, type="start")
subsetByOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, select="first")
findOverlaps(gr, gr1, select="last")
findOverlaps(gr1, gr)
findOverlaps(gr1, gr, type="start")
findOverlaps(gr1, gr, type="within")
findOverlaps(gr1, gr, type="equal")
## ---------------------------------------------------------------------
## MORE EXAMPLES
## ---------------------------------------------------------------------
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
## Overlaps between a GRanges and a GRangesList object:
table(!is.na(findOverlaps(grl, gr, select="first")))
countOverlaps(grl, gr)
findOverlaps(grl, gr)
subsetByOverlaps(grl, gr)
countOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, type="start")
subsetByOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, select="first")
table(!is.na(findOverlaps(grl, gr1, select="first")))
countOverlaps(grl, gr1)
findOverlaps(grl, gr1)
subsetByOverlaps(grl, gr1)
countOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, type="start")
subsetByOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, select="first")
## Overlaps between two GRangesList objects:
countOverlaps(grl, rev(grl))
findOverlaps(grl, rev(grl))
subsetByOverlaps(grl, rev(grl))
## ---------------------------------------------------------------------
## INTERPRETATION OF 'minoverlap' WHEN 'query' OR 'subject' IS A
## GRangesList OBJECT
## ---------------------------------------------------------------------
gr1 <- GRanges("chr5:1-26")
gr2 <- GRanges("chr5:31-40")
gr3 <- c(GRanges("chr5:11-20"), gr2)
grl123 <- GRangesList(gr1, gr2, gr3)
grl123
query <- GRanges("chr5:17-35")
findOverlaps(query, grl123[[1]], minoverlap=8) # 1 hit
findOverlaps(query, grl123[[2]], minoverlap=8) # no hit
findOverlaps(query, grl123[[3]], minoverlap=8) # no hit
## Using GRangesList object 'grl123' as the subject:
findOverlaps(query, grl123, minoverlap=8)
## As we can see, a hit is reported with the 3rd element in the subject.
## That's because the total number of positions in this overlap is 9:
## - positions 17 to 20 in the first range of grl123[[3]], so 4 positions
## - positions 31 to 35 in its second range, so 5 positions
## Sanity checks:
hits <- findOverlaps(query, grl123[[1]], minoverlap=8)
stopifnot(length(hits) == 1)
hits <- findOverlaps(query, grl123[[2]], minoverlap=8)
stopifnot(length(hits) == 0)
hits <- findOverlaps(query, grl123[[3]], minoverlap=8)
stopifnot(length(hits) == 0)
hits <- findOverlaps(query, grl123, minoverlap=8)
stopifnot(identical(subjectHits(hits), c(1L, 3L)))
hits <- findOverlaps(query, grl123, minoverlap=9)
stopifnot(identical(subjectHits(hits), c(1L, 3L)))
hits <- findOverlaps(query, grl123, minoverlap=10)
stopifnot(identical(subjectHits(hits), 1L))
hits <- findOverlaps(query, grl123, minoverlap=11)
stopifnot(length(hits) == 0)
Bioconductor/GenomicRanges documentation built on March 19, 2024, 12:39 p.m.
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| findOverlaps-methods | R Documentation |
Finding overlapping genomic ranges
Description
Various methods for finding/counting overlaps between objects containing genomic ranges. This man page describes the methods that operate on GenomicRanges and GRangesList objects.
NOTE: The findOverlaps generic function
and methods for IntegerRanges and
IntegerRangesList objects are defined and
documented in the IRanges package.
The methods for GAlignments,
GAlignmentPairs, and
GAlignmentsList objects are defined and
documented in the GenomicAlignments package.
GenomicRanges and GRangesList objects also support
countOverlaps, overlapsAny, and subsetByOverlaps
thanks to the default methods defined in the IRanges package and
to the findOverlaps and countOverlaps methods defined in
this package and documented below.
Usage
## S4 method for signature 'GenomicRanges,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GRangesList,GenomicRanges'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GRangesList'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GRangesList,GRangesList'
findOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges,GenomicRanges'
countOverlaps(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
ignore.strand=FALSE)
Arguments
query, subject |
A GRanges or GRangesList object. |
maxgap, minoverlap, type |
See IMPORTANT NOTE about how |
select |
When |
ignore.strand |
When set to |
Details
When the query and the subject are GRanges or
GRangesList objects, findOverlaps uses the triplet
(sequence name, range, strand) to determine which features (see
paragraph below for the definition of feature) from the query
overlap which features in the subject, where a strand value
of "*" is treated as occurring on both the "+" and
"-" strand.
An overlap is recorded when a feature in the query and a feature
in the subject have the same sequence name, have a compatible
pairing of strands (e.g. "+"/"+", "-"/"-",
"*"/"+", "*"/"-", etc.), and satisfy the
interval overlap requirements.
In the context of findOverlaps, a feature is a collection of
ranges that are treated as a single entity. For GRanges objects,
a feature is a single range; while for GRangesList objects,
a feature is a list element containing a set of ranges. In the results,
the features are referred to by number, which run from 1 to
length(query)/length(subject).
For type="equal" with GRangesList objects, query[[i]]
matches subject[[j]] iff for each range in query[[i]]
there is an identical range in subject[[j]], and vice versa.
Value
For findOverlaps: either a Hits object when
select="all" or an integer vector otherwise.
For countOverlaps: an integer vector containing the tabulated
query overlap hits.
Author(s)
P. Aboyoun, S. Falcon, M. Lawrence, and H. Pagès
See Also
The Hits class in the S4Vectors package for representing a set of hits between 2 vector-like objects.
The
findOverlapsgeneric function defined in the IRanges package.The GNCList constructor and class for preprocessing and representing a GenomicRanges or object as a data structure based on Nested Containment Lists.
The GRanges and GRangesList classes.
Examples
## ---------------------------------------------------------------------
## BASIC EXAMPLES
## ---------------------------------------------------------------------
## GRanges object:
gr <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
score=1:10,
GC=seq(1, 0, length=10)
)
gr
## GRangesList object:
gr1 <- GRanges(seqnames="chr2", ranges=IRanges(4:3, 6),
strand="+", score=5:4, GC=0.45)
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width=3),
strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(c(1, 4), c(3, 9)),
strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
grl <- GRangesList("gr1"=gr1, "gr2"=gr2, "gr3"=gr3)
## Overlapping two GRanges objects:
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
countOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, type="start")
subsetByOverlaps(gr, gr1, type="start")
findOverlaps(gr, gr1, select="first")
findOverlaps(gr, gr1, select="last")
findOverlaps(gr1, gr)
findOverlaps(gr1, gr, type="start")
findOverlaps(gr1, gr, type="within")
findOverlaps(gr1, gr, type="equal")
## ---------------------------------------------------------------------
## MORE EXAMPLES
## ---------------------------------------------------------------------
table(!is.na(findOverlaps(gr, gr1, select="arbitrary")))
countOverlaps(gr, gr1)
findOverlaps(gr, gr1)
subsetByOverlaps(gr, gr1)
## Overlaps between a GRanges and a GRangesList object:
table(!is.na(findOverlaps(grl, gr, select="first")))
countOverlaps(grl, gr)
findOverlaps(grl, gr)
subsetByOverlaps(grl, gr)
countOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, type="start")
subsetByOverlaps(grl, gr, type="start")
findOverlaps(grl, gr, select="first")
table(!is.na(findOverlaps(grl, gr1, select="first")))
countOverlaps(grl, gr1)
findOverlaps(grl, gr1)
subsetByOverlaps(grl, gr1)
countOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, type="start")
subsetByOverlaps(grl, gr1, type="start")
findOverlaps(grl, gr1, select="first")
## Overlaps between two GRangesList objects:
countOverlaps(grl, rev(grl))
findOverlaps(grl, rev(grl))
subsetByOverlaps(grl, rev(grl))
## ---------------------------------------------------------------------
## INTERPRETATION OF 'minoverlap' WHEN 'query' OR 'subject' IS A
## GRangesList OBJECT
## ---------------------------------------------------------------------
gr1 <- GRanges("chr5:1-26")
gr2 <- GRanges("chr5:31-40")
gr3 <- c(GRanges("chr5:11-20"), gr2)
grl123 <- GRangesList(gr1, gr2, gr3)
grl123
query <- GRanges("chr5:17-35")
findOverlaps(query, grl123[[1]], minoverlap=8) # 1 hit
findOverlaps(query, grl123[[2]], minoverlap=8) # no hit
findOverlaps(query, grl123[[3]], minoverlap=8) # no hit
## Using GRangesList object 'grl123' as the subject:
findOverlaps(query, grl123, minoverlap=8)
## As we can see, a hit is reported with the 3rd element in the subject.
## That's because the total number of positions in this overlap is 9:
## - positions 17 to 20 in the first range of grl123[[3]], so 4 positions
## - positions 31 to 35 in its second range, so 5 positions
## Sanity checks:
hits <- findOverlaps(query, grl123[[1]], minoverlap=8)
stopifnot(length(hits) == 1)
hits <- findOverlaps(query, grl123[[2]], minoverlap=8)
stopifnot(length(hits) == 0)
hits <- findOverlaps(query, grl123[[3]], minoverlap=8)
stopifnot(length(hits) == 0)
hits <- findOverlaps(query, grl123, minoverlap=8)
stopifnot(identical(subjectHits(hits), c(1L, 3L)))
hits <- findOverlaps(query, grl123, minoverlap=9)
stopifnot(identical(subjectHits(hits), c(1L, 3L)))
hits <- findOverlaps(query, grl123, minoverlap=10)
stopifnot(identical(subjectHits(hits), 1L))
hits <- findOverlaps(query, grl123, minoverlap=11)
stopifnot(length(hits) == 0)
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