# Visualization tools for gene fusions

## Documentation for package ‘chimeraviz’ version 1.14.0

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

## Help Pages

.fusions_to_gene_label_data | Create gene label data for RCircos from the given fusions.
.fusions_to_link_data | Create link data for RCircos from the given fusions.
.scale_list_to_interval | Scale a vector of numeric values to an interval.
add_fusion_reads_alignment | Add fusion reads alignment to fusion object
chimeraviz | chimeraviz: A package for working with and visualizing fusion genes.
chimeraviz-internals-fusions_to_gene_label_data | Create gene label data for RCircos from the given fusions.
chimeraviz-internals-fusions_to_link_data | Create link data for RCircos from the given fusions.
chimeraviz-internals-scaleListToInterval | Scale a vector of numeric values to an interval.
create_fusion_report | Create a Fusion Report
decide_transcript_category | Retrieves transcripts for partner genes in a Fusion object using Ensembldb
downstream_partner_gene | Get the downstream fusion partner gene
downstream_partner_gene-method | Get the downstream fusion partner gene
downstream_partner_gene<- | Get the downstream fusion partner gene
downstream_partner_gene<--method | Get the downstream fusion partner gene
down_shift | Remove introns and shift exons leftward
fetch_reads_from_fastq | Fetch reads from fastq files
Fusion | An S4 class to represent a fusion event.
Fusion-class | An S4 class to represent a fusion event.
fusion_spanning_reads_count | Get the spanning reads count from a Fusion object
fusion_spanning_reads_count-method | Get the spanning reads count from a Fusion object
fusion_split_reads_count | Get the split reads count from a Fusion object
fusion_split_reads_count-method | Get the split reads count from a Fusion object
fusion_to_data_frame | Coerce Fusion object to data.frame
get_ensembl_ids | Get ensembl ids for a fusion object
get_fusion_by_chromosome | Find fusions that involves genes in the given chromosome.
get_fusion_by_gene_name | Find fusions that includes the given gene.
get_fusion_by_id | Find a specific fusion object in a list by id
get_transcripts_ensembl_db | Retrieves transcripts for partner genes in a Fusion object using Ensembldb
import_aeron | Import results from an Aeron run into a list of Fusion objects.
import_chimpipe | Import results from a ChimPipe run into a list of Fusion objects.
import_defuse | Import results from a deFuse run into a list of Fusion objects.
import_ericscript | Import results from a EricScript run into a list of Fusion objects.
import_function_non_ucsc | Alternative import function for Gviz::AlignmentsTrack
import_fusioncatcher | Import results from a Fusioncatcher run into a list of Fusion objects.
import_fusionmap | Import results from a FusionMap run into a list of Fusion objects.
import_infusion | Import results from an InFusion run into a list of Fusion objects.
import_jaffa | Import results from a JAFFA run into a list of Fusion objects.
import_oncofuse | Import results from a oncofuse run into a list of Fusion objects.
import_prada | Import results from a PRADA run into a list of Fusion objects.
import_soapfuse | Import results from a SOAPfuse run into a list of Fusion objects.
import_squid | Import results from a SQUID run into a list of Fusion objects.
import_starfusion | 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
partner_gene_ensembl_id | Get the Ensembl ID from a PartnerGene object
partner_gene_ensembl_id-method | Get the Ensembl ID from a PartnerGene object
partner_gene_ensembl_id<- | Get the Ensembl ID from a PartnerGene object
partner_gene_ensembl_id<--method | Get the Ensembl ID from a PartnerGene object
partner_gene_junction_sequence | Get the junction sequence from a PartnerGene object
partner_gene_junction_sequence-method | Get the junction sequence from a PartnerGene object
plot_circle | Create a circle plot of the given fusions.
plot_fusion | Plot a fusion event with transcripts, coverage and ideograms.
plot_fusion_reads | Create a plot of the reads supporting the given fusion.
plot_fusion_separate | Plot a fusion event with transcripts, coverage and ideograms.
plot_fusion_together | Plot a fusion event with transcripts, coverage and ideograms.
plot_fusion_transcript | Plot possible fusion transcripts based on annotation.
plot_fusion_transcripts_graph | Graph plot of possible fusion transcripts.
plot_fusion_transcript_with_protein_domain | Plot a specific fusion transcript with protein domain annotations
plot_transcripts | Plot transcripts for each partner gene in a fusion event.
raw_chimpipe | ChimPipe data
raw_cytobandhg19 | Cytoband information HG19
raw_cytobandhg38 | Cytoband information HG138
raw_defuse | deFuse data
raw_ericscript | EricScript data
raw_fusion5267proteindomains | protein_domains_5267 bed file
raw_fusion5267reads | Fusion5267and11759 bamfile
raw_fusion5267readsBedGraph | Fusion5267and11759 bedGraph file
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_oncofuse | oncofuse data
raw_prada | PRADA data
raw_soapfuse | SOAPfuse data
raw_starfusion | STAR-Fusion data
select_transcript | 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.
split_on_utr_and_add_feature | Split GRanges object based on cds
upstream_partner_gene | Get the upstream fusion partner gene
upstream_partner_gene-method | Get the upstream fusion partner gene
upstream_partner_gene<- | Get the upstream fusion partner gene
upstream_partner_gene<--method | Get the upstream fusion partner gene
write_fusion_reference | Write fusion junction sequence to a fasta file