InteractionTrack-class: A class to hold chromatin interaction data for a specific...

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

A class to hold chromatin interaction data for a specific genomic region

Description

@slot giobject GenomicInteractions object from which the object was created

@slot variables list of chromosome, start, and end. Start and end can be NULL

@slot chromosome chromosome defined for the object

@slot stacking character

@slot dp DisplayPars for the object, access with 'availableDisplayPars()'

@slot name Object name

@slot imageMap NULL

Usage

## S4 method for signature 'InteractionTrack'
start(x)

## S4 method for signature 'InteractionTrack'
end(x)

## S4 method for signature 'InteractionTrack'
chromosome(GdObject)

## S4 method for signature 'InteractionTrack'
subset(x, from, to, chromosome, ...)

Arguments

x	An InteractionTrack object
GdObject	An InteractionTrack object
from	Integer start coordinate of subset region
to	Integer end coordinate of subset region
chromosome	Chromosome of subset region
...	additional arguments are ignored.

Details

InteractionTrack is a specific Gviz-derived class for enabling the visualisation of chromatin interaction data. The InteractionTrack class allows interactions on a specified chromosome to be visualised by examining interactions between anchors as bezier curves. The object is instantiated and used in a similar fashion to standard Gviz tracks and plotted using the plotTracks.

Several additional display parameters (i.e. displayPars(foo)=list(...) are defined for this class, including plot.anchors which can be used to specify whether anchors are to be drawn. col.anchors.line which can be used to alter the colour of border of these anchor elements and col.anchors.fill can be used to alter the fill colour of these elements.

The value of plot.outside determines whether or not interactions which span outside of the window are to be plotted, and col.outside defines the colour of these interactions. Similarly plot.trans determines whether trans-interactions are plotted and col.trans specifies the colour of trans-interactions.

By default, the height of an arc representing an interaction is proportional to the number of reads/counts supporting that interaction. Instead of using the counts to define this, the height can be set to be proportional to either fdr or p.value using the interaction.measure display parameter. By changing the interaction.dimension to width, the line widths of each arc now represent the statistic supporting them. The heights of the arcs can be made to be proportional to log10 of the supporting statistic by changing interaction.dimension.transform to log.

col.interactions sets the colour of arcs representing interactions within the region of interest. It is possible to colour the arcs by the type of interaction they are involved in (i.e. promoter-promoter interactions etc) by setting the col.interaction.types display parameter to be a named vector of colours, where the name corresponds to the type of interaction. This is applicable to anchors regions through the use of the col.anchors.line.node.class and col.anchors.fill.node.class parameters.

Functions

• start,InteractionTrack-method: Extract stored start position for object or, if that is NULL, minimum of region starts.

• end,InteractionTrack-method: Extract stored end position for object or, if that is NULL, maximum of region ends.

• chromosome,InteractionTrack-method: Extract stored chromosome of object

• subset,InteractionTrack-method: Subset the object to only contain interactions within the specified genomic region

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.