findOverlaps-methods: Finding overlapping genomic alignments
In GenomicAlignments: Representation and manipulation of short genomic alignments

Description Usage Arguments Details Value See Also Examples

Finds range overlaps between a GAlignments, GAlignmentPairs, or GAlignmentsList object, and another range-based object.

NOTE: The findOverlaps generic function and methods for IntegerRanges and IntegerRangesList objects are defined and documented in the IRanges package. The methods for GRanges and GRangesList objects are defined and documented in the GenomicRanges package.

GAlignments, GAlignmentPairs, and GAlignmentsList objects also support countOverlaps, overlapsAny, and subsetByOverlaps thanks to the default methods defined in the IRanges package and to the findOverlaps method defined in this package and documented below.

## S4 method for signature 'GAlignments,GAlignments'
findOverlaps(query, subject,
    maxgap=-1L, minoverlap=0L,
    type=c("any", "start", "end", "within"),
    select=c("all", "first", "last", "arbitrary"),
    ignore.strand=FALSE)

`query, subject`	A GAlignments, GAlignmentPairs, or GAlignmentsList object for either `query` or `subject`. A vector-like object containing ranges for the other one.
`maxgap, minoverlap, type, select`	See `?findOverlaps` in the IRanges package for a description of these arguments.
`ignore.strand`	When set to `TRUE`, the strand information is ignored in the overlap calculations.

When the query or the subject (or both) is a GAlignments object, it is first turned into a GRangesList object (with as( , "GRangesList")) and then the rules described previously apply. GAlignmentsList objects are coerced to GAlignments then to a GRangesList. Feature indices are mapped back to the original GAlignmentsList list elements.

When the query is a GAlignmentPairs object, it is first turned into a GRangesList object (with as( , "GRangesList")) and then the rules described previously apply.

A Hits object when select="all" or an integer vector otherwise.

findOverlaps.
Hits-class.
GRanges-class.
GRangesList-class.
GAlignments-class.
GAlignmentPairs-class.
GAlignmentsList-class.

ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn <- readGAlignments(ex1_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)

## Count alignments in 'galn' that DO overlap with 'subject' vs those
## that do NOT:
table(overlapsAny(galn, subject))
## Extract those that DO:
subsetByOverlaps(galn, subject)

## GAlignmentsList
galist <- GAlignmentsList(galn[8:10], galn[3000:3002])
gr <- GRanges(c("seq1", "seq1", "seq2"), 
              IRanges(c(15, 18, 1233), width=1),
              strand=c("-", "+", "+"))

countOverlaps(galist, gr)
countOverlaps(galist, gr, ignore.strand=TRUE)
findOverlaps(galist, gr)
findOverlaps(galist, gr, ignore.strand=TRUE)