findOverlaps-methods {GenomicRanges} | R Documentation |
Finds interval overlaps between a GRanges, GRangesList or GappedAlignments object and another object containing ranges.
## S4 method for signature 'GenomicRanges,GenomicRanges' findOverlaps(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), select = c("all", "first"), 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' subsetByOverlaps(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE) ## S4 method for signature 'GenomicRanges,GenomicRanges' match(x, table, nomatch = NA_integer_, incomparables = NULL) # Also: x %in% table
query, subject, x, table |
A GRanges, GRangesList or GappedAlignments
object. RangesList and RangedData
are also accepted for one of |
maxgap, minoverlap, type, select |
See |
ignore.strand |
When set to |
nomatch |
The integer value to be returned in the case when no match is found. |
incomparables |
This value is ignored. |
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 or the subject (or both) is a GappedAlignments
object, it is first turned into a GRangesList object (with
as( , "GRangesList")
) and then the rules described previously
apply.
For findOverlaps
either a RangesMatching object when
select = "all"
or an integer vector when select = "first"
.
For countOverlaps
an integer vector containing the tabulated
query overlap hits.
For subsetByOverlaps
an object of the same class as query
containing the subset that overlapped at least one entity in subject
.
For match
same as findOverlaps
when select = "first"
.
For %in%
the logical vector produced by
!is.na(match(x, table))
.
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 and H. Pages
findOverlaps
,
RangesMatching-class,
GRanges-class,
GRangesList-class,
GappedAlignments-class
## --------------------------------------------------------------------- ## WITH GRanges AND/OR GRangesList OBJECTS ## --------------------------------------------------------------------- ## 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(3, 6), strand = "+", score = 5L, 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)) grlist <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3) ## Overlapping two GRanges objects: table(gr %in% gr1) 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(gr1, gr) findOverlaps(gr1, gr, type = "start") findOverlaps(gr1, gr, type = "within") findOverlaps(gr1, gr, type = "equal") ## Overlapping a GRanges and a GRangesList object: table(grlist %in% gr) countOverlaps(grlist, gr) findOverlaps(grlist, gr) subsetByOverlaps(grlist, gr) countOverlaps(grlist, gr, type = "start") findOverlaps(grlist, gr, type = "start") subsetByOverlaps(grlist, gr, type = "start") findOverlaps(grlist, gr, select = "first") ## Overlapping two GRangesList objects: countOverlaps(grlist, rev(grlist)) findOverlaps(grlist, rev(grlist)) subsetByOverlaps(grlist, rev(grlist)) ## --------------------------------------------------------------------- ## WITH A GappedAlignments OBJECT ## --------------------------------------------------------------------- library(Rsamtools) # because file ex1.bam is in this package galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools") galn <- readGappedAlignments(galn_file) subject <- granges(galn)[1] ## Note the absence of query no. 9 (i.e. 'galn[9]') in this result: as.matrix(findOverlaps(galn, subject)) ## This is because, by default, findOverlaps()/countOverlaps() are ## strand specific: galn[8:10] countOverlaps(galn[8:10], subject) countOverlaps(galn[8:10], subject, ignore.strand=TRUE) ## Advanced examples: subsetByOverlaps(galn, subject) table(match(galn, subject), useNA = "ifany") table(galn %in% subject)