findOverlaps-methods {GenomicRanges} | R Documentation |
Finds interval overlaps between a GRanges, GIntervalTree, or GRangesList object, and another object containing ranges.
NOTE: The findOverlaps
generic function and methods
for Ranges and RangesList 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.
## S4 method for signature 'GenomicRanges,GenomicRanges' findOverlaps(query, subject, maxgap = 0L, minoverlap = 1L, 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 = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE) ## S4 method for signature 'GenomicRanges,GenomicRanges' overlapsAny(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE) ## S4 method for signature 'GenomicRanges,GenomicRanges' subsetByOverlaps(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE)
query, subject |
A GRanges or GRangesList object.
RangesList and RangedData are
also accepted for one of |
maxgap, minoverlap, type, select |
See |
ignore.strand |
When set to |
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. Strand is taken as "*"
for RangedData
and RangesList
.
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)
.
When the query is a GRanges or GRangesList object then
the subject can be a GIntervalTree object. For repeated queries against the same subject, it is more efficient to create a GIntervalTree
once for the subject using the GIntervalTree constructor described below and then perform the queries against
the GIntervalTree
instance. Note that GIntervalTree
objects are not supported for circular genomes.
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.
For overlapsAny
a logical vector of length equal to the number of
ranges in query
indicating those that overlap any of the ranges
in subject
.
For subsetByOverlaps
an object of the same class as query
containing the subset that overlapped at least one entity in subject
.
For RangedData
and RangesList
, with the exception of
subsetByOverlaps
, the results align to the unlisted
form of the object. This turns out to be fairly convenient for
RangedData
(not so much for RangesList
, but something
has to give).
P. Aboyoun, S. Falcon, M. Lawrence, N. Gopalakrishnan H. Pages and H. Corrada Bravo
## 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") ## using a GIntervalTree gtree <- GIntervalTree(gr1) table(!is.na(findOverlaps(gr, gtree, select="arbitrary"))) countOverlaps(gr, gtree) findOverlaps(gr, gtree) subsetByOverlaps(gr, gtree) ## Overlapping 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") ## using a GIntervalTree table(!is.na(findOverlaps(grl, gtree, select="first"))) countOverlaps(grl, gtree) findOverlaps(grl, gtree) subsetByOverlaps(grl, gtree) countOverlaps(grl, gtree, type = "start") findOverlaps(grl, gtree, type = "start") subsetByOverlaps(grl, gtree, type = "start") findOverlaps(grl, gtree, select = "first") ## Overlapping two GRangesList objects: countOverlaps(grl, rev(grl)) findOverlaps(grl, rev(grl)) subsetByOverlaps(grl, rev(grl))