InteractionSet (version 1.0.4)

Base Classes for Storing Genomic Interaction Data

Description

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

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Version

1.0.4

License

GPL-3

Maintainer

Aaron Lun

Last Published

February 15th, 2017

Functions in InteractionSet (1.0.4)

ContactMatrix subsetting

ContactMatrix subsetting and combining

Convert classes

Convert between classes

linkOverlaps

Link overlapping regions

Interaction overlaps

Find overlaps between interactions in one or two dimensions

ContactMatrix overlaps

Find overlaps between GRanges and a ContactMatrix

pairs

Extract paired ranges

ContactMatrix sorting

ContactMatrix sorting and ordering

Interaction distances

Get the linear distance for each interaction

GInteractions class

GInteractions class and constructors

Interaction compare

Interaction comparisons

Interaction subsetting

Interaction subsetting and combining

boundingBox

Get the bounding box

ContactMatrix accessors

InteractionSet class

InteractionSet class and constructors

Linearize interactions

Linearize 2D interactions into 1D ranges

ContactMatrix class

ContactMatrix class and constructors

GRanges methods

Equivalents of GRanges methods

ContactMatrix distances

Compute linear distances from ContactMatrix objects

Interaction accessors