pairs: Extract paired ranges

In LTLA/InteractionSet: Base Classes for Storing Genomic Interaction Data

Extract paired ranges

Description

Represent interactions in a GInteractions or Interaction object as a Pairs, SelfHits or GRangesList object.

Usage

## S4 method for signature 'GInteractions'
pairs(x, id=FALSE, as.grlist=FALSE)

# Equivalent call for InteractionSet to above.

makeGInteractionsFromGRangesPairs(x)

Arguments

x	For pairs, a GInteractions or InteractionSet object. For makeGInteractionsFromGRangesPairs, a Pairs object containing two parallel GRanges.
id	A logical scalar specifying whether indices should be returned instead of regions.
as.grlist	A logical scalar specifying whether a GRangesList should be returned.

Details

Recall that the GInteractions object stores anchor regions for each interaction in two parallel GRanges, where corresponding entries between the two GRanges constitute the pair of regions for one interaction. These parallel ranges can be extracted and stored as a Pairs object for further manipulation. This is similar to the GRangesList reported by anchors with type="both" and id=FALSE. The reverse conversion is performed using makeGInteractionsFromGRangesPairs.

An alternative representation involves storing the two anchors for each interaction in a single GRanges of length 2. Multiple interactions are then stored as a GRangesList, along with any metadata and sequence information. This is returned if as.grlist=FALSE, may be more useful in some applications where the two interacting regions must be in the same GRanges. Finally, if id=TRUE, the anchor indices are extracted and returned as a SelfHits object. This may be useful for graph construction.

Value

For pairs, if id=TRUE, a SelfHits object is returned. Otherwise, if as.grlist=TRUE, a GRangesList object is returned. Otherwise, a Pairs object is returned.

For makeGInteractionsFromGRangesPairs, a GInteractions object is returned.

Author(s)

Aaron Lun

See Also

GInteractions, Pairs, SelfHits, GRangesList

Examples

example(GInteractions, echo=FALSE)
y <- pairs(gi)
y
makeGInteractionsFromGRangesPairs(y)

pairs(gi, id=TRUE)
pairs(gi, as.grlist=TRUE)

example(InteractionSet, echo=FALSE)
pairs(iset)
pairs(iset, id=TRUE)
pairs(iset, as.grlist=TRUE)

LTLA/InteractionSet documentation built on July 3, 2023, 8:44 a.m.