1 Introduction

This is the vignette of chimeraviz, an R package that automates the creation of chimeric RNA visualizations. This vignette will take you through the functionality of chimeraviz.

2 Basic features

chimeraviz allows you to import data from nine different fusion-finders: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPFuse, and STAR-FUSION. Getting started is easy:

# Load chimeraviz
library(chimeraviz)

# Get reference to results file from deFuse
defuse833ke <- system.file(
"extdata",
"defuse_833ke_results.filtered.tsv",
package="chimeraviz")

# Load the results file into a list of fusion objects
fusions <- import_defuse(defuse833ke, "hg19")

Import functions for the other supported fusion-finders are similarly named (for example importEriscript or importInfusion).

A list of Fusion objects, objects that represent each fusion transcript, is now available in the list fusions.

length(fusions)

## [1] 17

As you can see, this list has 17 fusion objects. It is straightforward to find a specific fusion event and print information about it, or about each of the partner genes.

# Find a specific fusion event
fusion <- get_fusion_by_id(fusions, 5267)

# Show information about this fusion event
fusion

## [1] "Fusion object"
## [1] "id: 5267"
## [1] "Fusion tool: defuse"
## [1] "Genome version: hg19"
## [1] "Gene names: RCC1-HENMT1"
## [1] "Chromosomes: chr1-chr1"
## [1] "Strands: +,-"
## [1] "In-frame?: FALSE"

# Show information about the upstream fusion partner
upstream_partner_gene(fusion)

## [1] "PartnerGene object"
## [1] "Name: RCC1"
## [1] "ensemblId: ENSG00000180198"
## [1] "Chromosome: chr1"
## [1] "Strand: +"
## [1] "Breakpoint: 28834672"

# Show information about the downstream fusion partner
downstream_partner_gene(fusion)

## [1] "PartnerGene object"
## [1] "Name: HENMT1"
## [1] "ensemblId: ENSG00000162639"
## [1] "Chromosome: chr1"
## [1] "Strand: -"
## [1] "Breakpoint: 109202584"

3 Plotting