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

In stianlagstad/chimeraviz: Visualization tools for gene fusions

An S4 class to represent a gene partner in a fusion

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.

stianlagstad/chimeraviz documentation built on Dec. 3, 2023, 8:11 p.m.