findOverlaps-methods: Finding overlapping genomic ranges

In vjcitn/GenomicRangesGHA: Representation and manipulation of genomic intervals; demo with github actions binary generation

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 '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.
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 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))

vjcitn/GenomicRangesGHA documentation built on Jan. 18, 2021, 12:39 a.m.