Interaction distances {InteractionSet} | R Documentation

## Get the linear distance for each interaction

### Description

Compute the distance between interacting regions on the linear genome, for each pairwise interaction contained in a GInteractions or InteractionSet object.

### Usage

    ## S4 method for signature 'GInteractions'
    pairdist(x, type="mid")
    ## S4 method for signature 'InteractionSet'
    pairdist(x, type="mid")

    ## S4 method for signature 'GInteractions'
    intrachr(x)
    ## S4 method for signature 'InteractionSet'
    intrachr(x)

### Arguments

`x` | A GInteractions or InteractionSet object.
`type` | A character string specifying the type of distance to compute. Can take values of `"mid"`, `"gap"`, `"span"`, `"diag"` or `"intra"`.

### Details

For each interaction in `x`, the `pairdist` method computes the distance between the two interacting regions. An integer vector is returned, with values computed according to the specified value of `type`:

`"mid"`:

  The distance between the midpoints of the two regions (rounded down to the nearest integer) is returned.

`"gap"`:

  The length of the gap between the closest points of the two regions is computed - negative lengths are returned for overlapping regions, indicating the length of the overlap.

`"span"`:

  The distance between the furthermost points of the two regions is computed.

`"diag"`:

  The difference between the anchor indices is returned. This corresponds to a diagonal on the interaction space when bins are used in the `regions` slot of `x`.

Interchromosomal interactions are marked with `NA`. Alternatively, if `type="intra"`, a logical vector is returned indicating whether the interaction occurs between two regions on the same chromosome. `intrachr(x)` is an alias for `pairdist(x, type="intra")`.

The return values of the assorted methods are the same for both GInteractions and InteractionSet objects. Methods for the latter operate on the GInteractions object in the `interactions` slot.

### Value

An integer or logical vector of distances.

### Author(s)

Aaron Lun

### See Also

`GInteractions-class`, `InteractionSet-class`

### Examples

    example(GInteractions, echo=FALSE)

    pairdist(gi)
    pairdist(gi, type="gap")
    pairdist(gi, type="span")
    pairdist(gi, type="diag")
    intrachr(gi)

    example(InteractionSet, echo=FALSE)

    pairdist(iset)
    pairdist(iset, type="gap")
    pairdist(iset, type="span")
    pairdist(iset, type="diag")
    intrachr(iset)

[Package InteractionSet version 1.12.0 Index]