# Visualization tools for gene fusions

## Documentation for package ‘chimeraviz’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

chimeraviz-package | chimeraviz: A package for working with and visualizing fusion genes.
.fusionsToGeneLabelData | Create gene label data for RCircos from the given fusions.
.fusionsToLinkData | Create link data for RCircos from the given fusions.
.scaleListToInterval | Scale a vector of numeric values to an interval.
addFusionReadsAlignment | Add fusion reads alignment to fusion object
chimeraviz | chimeraviz: A package for working with and visualizing fusion genes.
chimeraviz-internals-fusionsToGeneLabelData | Create gene label data for RCircos from the given fusions.
chimeraviz-internals-fusionsToLinkData | Create link data for RCircos from the given fusions.
chimeraviz-internals-scaleListToInterval | Scale a vector of numeric values to an interval.
createFusionReport | Create a Fusion Report
decideTranscriptCategory | Retrieves transcripts for partner genes in a Fusion object using Ensembldb
downstreamPartnerGene | Get the downstream fusion partner gene
downstreamPartnerGene-method | Get the downstream fusion partner gene
downstreamPartnerGene<- | Get the downstream fusion partner gene
downstreamPartnerGene<--method | Get the downstream fusion partner gene
fetchReadsFromFastq | Fetch reads from fastq files
Fusion | An S4 class to represent a fusion event.
Fusion-class | An S4 class to represent a fusion event.
fusionSpanningReadsCount | Get the spanning reads count from a Fusion object
fusionSpanningReadsCount-method | Get the spanning reads count from a Fusion object
fusionSplitReadsCount | Get the split reads count from a Fusion object
fusionSplitReadsCount-method | Get the split reads count from a Fusion object
fusionToDataFrame | Coerce Fusion object to data.frame
getEnsemblIds | Get ensembl ids for a fusion object
getFusionByChromosome | Find fusions that involves genes in the given chromosome.
getFusionByGeneName | Find fusions that includes the given gene.
getFusionById | Find a specific fusion object in a list by id
getTranscriptsEnsembldb | Retrieves transcripts for partner genes in a Fusion object using Ensembldb
importDefuse | Import results from a deFuse run into a list of Fusion objects.
importEricscript | Import results from a EricScript run into a list of Fusion objects.
importFunctionNonUCSC | Alternative import function for Gviz::AlignmentsTrack
importFusioncatcher | Import results from a Fusioncatcher run into a list of Fusion objects.
importFusionmap | Import results from a FusionMap run into a list of Fusion objects.
importInfusion | Import results from an InFusion run into a list of Fusion objects.
importJaffa | Import results from a JAFFA run into a list of Fusion objects.
importPrada | Import results from a PRADA run into a list of Fusion objects.
importSoapfuse | Import results from a SOAPfuse run into a list of Fusion objects.
importStarfusion | Import results from a STAR-Fusion run into a list of Fusion objects.
PartnerGene | An S4 class to represent a gene partner in a fusion
PartnerGene-class | An S4 class to represent a gene partner in a fusion
partnerGeneEnsemblId | Get the Ensembl ID from a PartnerGene object
partnerGeneEnsemblId-method | Get the Ensembl ID from a PartnerGene object
partnerGeneEnsemblId<- | Get the Ensembl ID from a PartnerGene object
partnerGeneEnsemblId<--method | Get the Ensembl ID from a PartnerGene object
partnerGeneJunctionSequence | Get the junction sequence from a PartnerGene object
partnerGeneJunctionSequence-method | Get the junction sequence from a PartnerGene object
plotCircle | Create a circle plot of the given fusions.
plotFusion | Plot a fusion event with transcripts, coverage and ideograms.
plotFusionReads | Create a plot of the reads supporting the given fusion.
plotFusionSeparate | Plot a fusion event with transcripts, coverage and ideograms.
plotFusionTogether | Plot a fusion event with transcripts, coverage and ideograms.
plotFusionTranscript | Plot possible fusion transcripts based on annotation.
plotFusionTranscriptsGraph | Graph plot of possible fusion transcripts.
plotTranscripts | Plot transcripts for each partner gene in a fusion event.
raw_cytobandhg19 | Cytoband information HG19
raw_cytobandhg38 | Cytoband information HG138
raw_defuse | deFuse data
raw_ericscript | EricScript data
raw_fusion5267reads | Fusion5267and11759 bamfile
raw_fusioncatcher | Fusioncatcher data
raw_fusionmap | FusionMap data
raw_Homo_sapiens.GRCh37.74 | Homo_sapiens.GRCh37.74_subset.gtf
raw_infusion | InFusion data
raw_jaffa | JAFFA data
raw_prada | PRADA data
raw_soapfuse | SOAPfuse data
raw_starfusion | STAR-Fusion data
selectTranscript | Select which transcript to use (for plotting) for a GenePartner object
show-method | Show method for the Fusion class.
show-method | Show method for the PartnerGene class.
splitOnUtrAndAddFeature | Split GRanges object based on cds
upstreamPartnerGene | Get the upstream fusion partner gene
upstreamPartnerGene-method | Get the upstream fusion partner gene
upstreamPartnerGene<- | Get the upstream fusion partner gene
upstreamPartnerGene<--method | Get the upstream fusion partner gene
writeFusionReference | Write fusion junction sequence to a fasta file