distances: Get the linear distance for each interaction

In InteractionSet: Base Classes for Storing Genomic Interaction Data

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)

InteractionSet documentation built on April 17, 2021, 6 p.m.