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.

fusion_tool

Name of the fusion tool.

genome_version

Name of the genome used to map reads.

spanning_reads_count

The number of spanning reads supporting the fusion.

split_reads_count

The number of split reads supporting the fusion.

fusion_reads_alignment

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

gene_upstream

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

gene_downstream

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.

fusion_tool_specific_data

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.