linkOverlaps {InteractionSet} | R Documentation

## Link overlapping regions

### Description

Identify interactions that link two sets of regions by having anchor regions overlapping one entry in each set.

### Usage

    ## S4 method for signature 'GInteractions,Vector,Vector'
    linkOverlaps(query, subject1, subject2, ...,
        ignore.strand=TRUE, use.region="both")

### Arguments

`query` | A GInteractions or InteractionSet object.
`subject1, subject2` | A Vector object defining a set of genomic intervals, such as a GRanges or GRangesList. `subject2` may be missing. Alternatively, both `subject1` and `subject2` may be Hits objects, see below.
`..., ignore.strand` | Additional arguments to be passed to `findOverlaps`. Note that `ignore.strand=TRUE` by default, as genomic interactions are usually unstranded.
`use.region` | A string specifying which `query` regions should be used to overlap which `subject`. Ignored if `subject2` is missing.

### Details

This function identifies all interactions in `query` where one anchor overlaps an entry in `subject1` and the other anchor overlaps an entry in `subject2`. It is designed to be used to identify regions that are linked by interactions in `query`. For example, one might specify genes as `subject1` and enhancers as `subject2`, to identify all gene-enhancer contacts present in `query`. This is useful when the exact pairings between `subject1` and `subject2` are undefined.

The function returns a DataFrame specifying the index of the interaction in `query`; the index of the overlapped region in `subject1`; and the index of the overlapped region in `subject2`. If multiple regions in `subject1` and/or `subject2` are overlapping the anchor regions of a particular interaction, all combinations of two overlapping regions (one from each `subject*` set) are reported for that interaction.

By default, `use.region="both"` such that overlaps will be considered between any first/second interacting region in `query` and either `subject1` or `subject2`. If `use.region="same"`, overlaps will only be considered between the first interacting region in `query` and entries in `subject1`, and between the second interacting region and `subject2`. The opposite applies with `use.region="reverse"`, where the first and second interacting regions are overlapped with `subject2` and `subject1` respectively.

If `subject2` is not specified, links within `subject1` are identified instead, i.e., `subject2` is set to `subject1`. In such cases, the returned DataFrame is such that the first subject index is always greater than the second subject index, to avoid redundant permutations.

### Value

A DataFrame of integer indices indicating which elements of `query` link which elements of `subject1` and `subject2`.

### Using Hits as input

Hits objects can be used for the `subject1` and `subject2` arguments. These should be constructed using `findOverlaps` with `regions(query)` as the query and the genomic regions of interest as the subject. For example, the calls below:

    > linkOverlaps(query, subject1) # 1
    > linkOverlaps(query, subject1, subject2) # 2

will yield exactly the same output as:

    > olap1 <- findOverlaps(regions(query), subject1)
    > linkOverlaps(query, olap1) # 1
    > olap2 <- findOverlaps(regions(query), subject2)
    > linkOverlaps(query, olap1, olap2) # 2

This is useful in situations where `regions(query)` and the genomic regions in `subject1` and `subject2` are constant across multiple calls to `linkOverlaps`. In such cases, the overlaps only need to be calculated once, avoiding redundant work within `linkOverlaps`.

### Author(s)

Aaron Lun

### See Also

`findOverlaps,GInteractions,Vector-method`

### Examples

    example(GInteractions, echo=FALSE)

    all.genes <- GRanges("chrA", IRanges(0:9*10, 1:10*10))
    all.enhancers <- GRanges("chrB", IRanges(0:9*10, 1:10*10))

    out <- linkOverlaps(gi, all.genes, all.enhancers)
    head(out)

    out <- linkOverlaps(gi, all.genes)
    head(out)

    # Same methods apply for InteractionSet objects.

    example(InteractionSet, echo=FALSE)
    out <- linkOverlaps(iset, all.genes, all.enhancers)
    out <- linkOverlaps(iset, all.genes)

[Package InteractionSet version 1.10.0 Index]