PartnerGene-class: An S4 class to represent a gene partner in a fusion

In chimeraviz: Visualization tools for gene fusions

Description

The PartnerGene class represents one of the genes in a fusion event.

Slots

name

Character containing name of the gene.

ensembl_id

Character containing ensembl id for the gene.

chromosome

Character containing chromosome name.

breakpoint

Numeric containing the fusion breakpoint.

strand

Character containing gene strand.

junction_sequence

Biostrings::DNAString containing the sequence right before/after the fusion breakpoint.

transcripts

GenomicRanges::GRangesList containing three GenomicRanges::Granges() objects, one for each "transcript type". The transcript types are: 1) Transcripts where the fusion breakpoint hits an exon boundary, 2) transcripts where the fusion breakpoint is within an exon, 3) transcripts where the fusion breakpoint is within an intron.

chimeraviz documentation built on Jan. 19, 2021, 2 a.m.