InteractionSet (version 1.0.4)

GRanges methods: Equivalents of GRanges methods

Description

Methods for GInteractions, InteractionSet and ContactMatrix that operate on the internal GenomicRanges.

Usage

"trim"(x, use.names=FALSE)
"width"(x)
# Equivalent calls for InteractionSet and ContactMatrix.

Arguments

x

A GInteractions, InteractionSet or ContactMatrix object.

use.names

See ?"trim,GenomicRanges-method".

Value

Depending on the method, an object of the same class as x, or information regarding the genomic regions -- see Details.

Details

The trim method will return an object of the same class as x where out-of-bound ranges in regions(x) are truncated to fit. This is followed by resorting of the regions and removal of redundant regions. As such, that the length of regions(x) and the anchor indices for each interaction may change before and after trimming. However, the number and order of the interactions will not change.

For GInteractions and InteractionSet objects, the width method will return a DataFrame with integer fields anchor1 and anchor2. Each row contains the width of the two anchor regions corresponding to each interaction. For ContactMatrix objects, the method will return a list with the same fields (a different format is necessary as the lengths of anchor1 and anchor2 may be different).

See Also

trim, width

Examples

example(GInteractions, echo=FALSE)

trim(gi)
width(gi)

example(ContactMatrix, echo=FALSE)
trim(x)
width(x)