Visualization tools for gene fusions

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Documentation for package ‘chimeraviz’ version 1.34.0

• 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