interaction-bind: Interaction combining

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

Interaction combining

Description

Methods to combine InteractionSet or GInteractions objects.

Usage

## S4 method for signature 'GInteractions'
c(x, ..., recursive=FALSE)

## S4 method for signature 'InteractionSet'
rbind(..., deparse.level=1)
## S4 method for signature 'InteractionSet'
cbind(..., deparse.level=1)

Arguments

x	A GInteractions or InteractionSet object.
...	For rbind and c, ... contains GInteractions or InteractionSet objects to be combined row-wise. All objects must be of the same class. For c, any objects are additional to that already specified in x. For cbind, ... contains InteractionSet objects to be combined column-wise.
deparse.level	An integer scalar; see ?base::cbind for a description of this argument.
recursive	An integer scalar, ignored.

Value

A combined object of the same class as x.

Details for GInteractions

c will concatenate GInteractions objects. It will check whether the regions slot of all supplied objects are the same, in which case the regions and anchor indices are used directly. Otherwise, the regions slot is set to a new GRanges object consisting of the (sorted) union of all regions across the input objects. Anchor indices in each object are refactored appropriately to refer to the relevant entries in the new GRanges.

Note that the column names in mcols must be identical across all supplied objects. The column names of mcols for the regions slot must also be identical across objects. If GInteractions objects of different strictness (i.e., StrictGInteractions and ReverseGInteractions) are concatenated, the returned object will be of the same class as the first supplied object.

Details for InteractionSet

cbind will combine objects with the same interactions but different samples. Errors will occur if the interactions are not identical between objects (i.e., must have same values in the interactions slots). Additional restrictions apply on the column and assay names - see cbind,SummarizedExperiment-method for details.

rbind will combine objects with the same samples but different interactions. In this case, the interactions need not be identical, and will be concatenated using the methods described above for GInteractions objects. Again, additional restrictions apply - see rbind,SummarizedExperiment-method for details.

Author(s)

Aaron Lun

See Also

InteractionSet-class GInteractions-class

Examples

example(GInteractions, echo=FALSE)
c(gi, gi)

new.gi <- gi
regions(new.gi) <- resize(regions(new.gi), width=20, fix="start")
c(gi, new.gi)

#################
# Same can be done for an InteractionSet object:

example(InteractionSet, echo=FALSE)
cbind(iset, iset)
rbind(iset, iset)

new.iset <- iset
regions(new.iset) <- resize(regions(new.iset), width=20, fix="start")
rbind(iset, new.iset)

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