An S4 class to represent a fusion event.

Description

The Fusion class represents a fusion event, holding data imported from a fusion tool.

Slots

id

A unique id representing a fusion event. For deFuse data this will be the cluster id.

fusionTool

Name of the fusion tool.

genomeVersion

Name of the genome used to map reads.

spanningReadsCount

The number of spanning reads supporting the fusion.

splitReadsCount

The number of split reads supporting the fusion.

fusionReadsAlignment

A Gviz::AlignmentsTrack object holding the fusion reads aligned to the fusion sequence.

geneA

A PartnerGene object holding information of the upstream fusion partner gene.

geneB

A PartnerGene object holding information of the downstream fusion partner gene.

inframe

A logical value indicating whether or not the downstream fusion partner gene is inframe or not. Not all fusion-finders report this.

fusionToolSpecificData

A list that will hold fields of importance for a specific fusion finder. This field is used because many fusion-finders report important values that are hard to fit into a standardized format. Examples of values that are added to this list is probability from deFuse and EricScore from EricScript.