findOverlaps-methods {GenomicTuples} | R Documentation

## Finding overlapping genomic tuples

### Description

Various methods for finding/counting overlaps between objects containing genomic tuples. This man page describes the methods that operate on GTuples and GTuplesList objects.

NOTE: The `findOverlaps` generic function is defined and documented in the IRanges package. The `findOverlaps` method for GenomicRanges and GRangesList objects are defined and documented in the GenoicRanges package.

GTuples and GTuplesList 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 'GTuples,GTuples'
    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 'GTuples,GTuples'
    countOverlaps(query, subject,
        maxgap = -1L, minoverlap = 0L,
        type = c("any", "start", "end", "within", "equal"),
        ignore.strand = FALSE)

### Arguments

`query, subject` | A `GTuples` or `GTuplesList` object.
`type` | See details below.
`maxgap, minoverlap` | 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

The `findOverlaps`-based methods involving genomic tuples, either through `GTuples` or `GTuplesList` objects, can search for tuple-tuple, tuple-range and range-tuple overlaps. Each of these are described below, with attention paid to the important special case of finding "equal tuple-tuple overlaps".

Equal tuple-tuple overlaps

  When the `query` and the `subject` are both `GTuples` objects and `type = "equal"`, `findOverlaps` uses the seqnames (`seqnames`), positions (`tuples,GTuples-method`) and strand (`strand`) to determine which tuples from the `query` exactly match those in the `subject`, where a `strand` value of `"*"` is treated as occurring on both the `"+"` and `"-"` strand. An overlap is recorded when a tuple in the `query` and a tuple in the `subject` have the same sequence name, have a compatible pairing of strands (e.g. `"+"`/`"+"`, `"-"`/`"-"`, `"*"`/`"+"`, `"*"`/`"-"`, etc.), and have identical positions.

  NOTE: Equal tuple-tuple overlaps can only be computed if `size(query)` is equal to `size(subject)`.

Other tuple-tuple overlaps

  When the `query` and the `subject` are `GTuples` or `GTuplesList` objects and `type = "any"`, `"start"`, `"end"` or `"within"`, `findOverlaps` treats the tuples as if they were ranges, with ranges given by [pos_{1}, pos_{m}] and where m is the `size,GTuples-method` of the tuples. This is done via inheritance so that a `GTuples` (resp. `GTuplesList`) object is treated as a `GRanges` (resp. `GRangesList`) and the appropriate `findOverlaps` method is dispatched upon.

  NOTE: This is the only type of overlap finding available when either the `query` and `subject` are `GTuplesList` objects. This is following the behaviour of `findOverlaps,GRangesList,GRangesList-method` that allows `type = "any"`, `"start"`, `"end"` or `"within"` but does not allow `type = "equal"`.

tuple-range and range-tuple overlaps

  When one of the `query` and the `subject` is not a `GTuples` or `GTuplesList` objects, `findOverlaps` treats the tuples as if they were ranges, with ranges given by [pos_{1}, pos_{m}] and where m is the `size,GTuples-method` of the tuples. This is done via inheritance so that a `GTuples` (resp. `GTuplesList`) object is treated as a `GRanges` (resp. `GRangesList`) and the appropriate `findOverlaps` method is dispatched upon.

In the context of `findOverlaps`, a feature is a collection of tuples/ranges that are treated as a single entity. For `GTuples` objects, a feature is a single tuple; while for `GTuplesList` objects, a feature is a list element containing a set of tuples. In the results, the features are referred to by number, which run from 1 to `length(query)`/`length(subject)`.

### 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.

For `overlapsAny` a logical vector of length equal to the number of tuples/ranges in `query` indicating those that overlap any of the tuples/ranges in `subject`.

For `subsetByOverlaps` an object of the same class as `query` containing the subset that overlapped at least one entity in `subject`.

### Author(s)

Peter Hickey for methods involving `GTuples` and `GTuplesList`. P. Aboyoun, S. Falcon, M. Lawrence, N. Gopalakrishnan, H. Pagès and H. Corrada Bravo for all the real work underlying the powerful `findOverlaps` functionality.

### See Also

- Please see the package vignette for an extended discussion of overlaps involving genomic tuples, which is available by typing `vignette(topic = 'GenomicTuplesIntroduction', package = 'GenomicTuples')` at the R prompt.

- `findOverlaps`

- `findOverlaps`

- `Hits-class`

- `GTuples-class`

- `GTuplesList-class`

- `GRanges-class`

- `GRangesList-class`

### Examples

    ## GTuples object containing 3-tuples:
    gt3 <- GTuples(seqnames = c('chr1', 'chr1', 'chr1', 'chr1', 'chr2'),
                   tuples = matrix(c(10L, 10L, 10L, 10L, 10L, 20L, 20L, 20L, 25L,
                                     20L, 30L, 30L, 35L, 30L, 30L), ncol = 3),
                   strand = c('+', '-', '*', '+', '+'))

    ## GTuplesList object
    gtl3 <- GTuplesList(A = gt3[1:3], B = gt3[4:5])

    ## Find equal genomic tuples:
    findOverlaps(gt3, gt3, type = 'equal')
    ## Note that this is different to the results if the tuples are treated as
    ## ranges since this ignores the "internal positions" (pos2):
    findOverlaps(granges(gt3), granges(gt3), type = 'equal')

    ## Scenarios where tuples are treated as ranges:
    findOverlaps(gt3, gt3, type = 'any')
    findOverlaps(gt3, gt3, type = 'start')
    findOverlaps(gt3, gt3, type = 'end')
    findOverlaps(gt3, gt3, type = 'within')

    ## Overlapping a GTuples and a GTuplesList object (tuples treated as ranges):
    table(!is.na(findOverlaps(gtl3, gt3, select="first")))
    countOverlaps(gtl3, gt3)
    findOverlaps(gtl3, gt3)
    subsetByOverlaps(gtl3, gt3)
    countOverlaps(gtl3, gt3, type = "start")
    findOverlaps(gtl3, gt3, type = "start")
    subsetByOverlaps(gtl3, gt3, type = "start")
    findOverlaps(gtl3, gt3, select = "first")

[Package GenomicTuples version 1.18.1 Index]