| Title: | Visualization tools for gene fusions |
|---|---|
| Description: | chimeraviz manages data from fusion gene finders and provides useful visualization tools. |
| Authors: | Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M. Hoff [ctb], Bjarne Johannessen [ctb], Ole Christian Lingjærde [ctb], Rolf Skotheim [ctb] |
| Maintainer: | Stian Lågstad <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.31.0 |
| Built: | 2024-06-30 06:17:10 UTC |
| Source: | https://github.com/bioc/chimeraviz |
This function lets you add a fusion read alignment file to a fusion object. If you've mapped the reads supporting a fusion against the fusion junction sequence, and have the resulting bamfile, use this function to add the information (as a Gviz::GAlignmentPairs object) to the fusion object.
add_fusion_reads_alignment(fusion, bamfile)add_fusion_reads_alignment(fusion, bamfile)
fusion |
The fusion object to add a genomic alignment to. |
bamfile |
The bam file containing the fusion reads plotted to the fusion sequence. |
An updated fusion object with fusion@fusion_reads_alignment set.
# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) # Find the specific fusion we have aligned reads for fusion <- get_fusion_by_id(fusions, 5267) # Get reference to the bamfile with the alignment data bamfile5267 <- system.file( "extdata", "5267readsAligned.bam", package="chimeraviz") # Add the bam file of aligned fusion reads to the fusion object fusion <- add_fusion_reads_alignment(fusion, bamfile5267)# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) # Find the specific fusion we have aligned reads for fusion <- get_fusion_by_id(fusions, 5267) # Get reference to the bamfile with the alignment data bamfile5267 <- system.file( "extdata", "5267readsAligned.bam", package="chimeraviz") # Add the bam file of aligned fusion reads to the fusion object fusion <- add_fusion_reads_alignment(fusion, bamfile5267)
chimeraviz manages data from fusion gene finders and provides useful visualization tools.
This function takes a list of Fusion objects and creates a data frame in the format that RCircos.Gene.Name.Plot() expects for gene label data.
.fusions_to_gene_label_data(fusion_list).fusions_to_gene_label_data(fusion_list)
fusion_list |
A list of Fusion objects. |
A data frame with fusion gene label data compatible with RCircos.Gene.Name.Plot()
# @examples # Apparently examples shouldn't be set on private functions defuse833ke <- system.file("extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) labelData <- chimeraviz::.fusions_to_gene_label_data(fusions) # This labelData can be used with RCircos.Gene.Connector.Plot() and RCircos.Gene.Name.Plot()
This function takes a list of Fusion objects and creates a data frame in the format that RCircos::RCircos.Link.Plot() expects for link data.
.fusions_to_link_data(fusion_list, min_link_width = 1, max_link_widt = 10).fusions_to_link_data(fusion_list, min_link_width = 1, max_link_widt = 10)
fusion_list |
A list of Fusion objects. |
min_link_width |
The minimum link line width. Default = 1 |
max_link_widt |
The maximum link line width. Default = 10 |
A data frame with fusion link data compatible with RCircos::RCircos.Link.Plot()
# @examples # Apparently examples shouldn't be set on private functions defuse833ke <- system.file("extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) linkData <- chimeraviz::.fusions_to_link_data(fusions) # This linkData can be used with RCircos::RCircos.Link.Plot()
This function takes a vector of numeric values as well as an interval [new_min, new_max] that the numeric values will be scaled (normalized) to.
.scale_list_to_interval(the_list, new_min, new_max).scale_list_to_interval(the_list, new_min, new_max)
the_list |
A vector of numeric values. |
new_min |
Minimum value for the new interval. |
new_max |
Maximum value for the new interval. |
A data frame with fusion link data compatible with RCircos::RCircos.Link.Plot()
# @examples # Apparently examples shouldn't be set on private functions list012 <- c(0,1,2) .scale_list_to_interval(list012, 1, 3) # [1] 1 2 3
This function will create a html report with an overplot and a sortable, searchable table with the fusion data.
create_fusion_report(fusions, output_filename, quiet = TRUE)create_fusion_report(fusions, output_filename, quiet = TRUE)
fusions |
A list of Fusion objects. |
output_filename |
Output html-file filename. |
quiet |
Parameter passed to rmarkdown::render() to toggle its output. |
Creates a html report with an overplot and a sortable, searchable table with the fusion data.
# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # Temporary file to store the report random_filename <- paste0( paste0(sample(LETTERS, 5, replace = TRUE), collapse=''), ".png" ) # Create report create_fusion_report(fusions, random_filename) # Delete the file file.remove(random_filename)# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # Temporary file to store the report random_filename <- paste0( paste0(sample(LETTERS, 5, replace = TRUE), collapse=''), ".png" ) # Create report create_fusion_report(fusions, random_filename) # Delete the file file.remove(random_filename)
This function will check where in the transcript (the GRanges object) the fusion breakpoint is located, and return either "exonBoundary", "withinExon", "withinIntron", or "intergenic".
decide_transcript_category(gr, fusion)decide_transcript_category(gr, fusion)
gr |
The GRanges object containing the transcript to be checked. |
fusion |
The fusion object used to check the transcript. |
Either "exonBoundary", "withinExon", "withinIntron", or "intergenic" depending on where in the transcript the breakpoint hits.
# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get all exons for all transcripts in the genes in the fusion transcript allTranscripts <- ensembldb::exonsBy( edb, filter = list( AnnotationFilter::GeneIdFilter( c( partner_gene_ensembl_id(upstream_partner_gene(fusion)), partner_gene_ensembl_id(downstream_partner_gene(fusion))))), columns = c( "gene_id", "gene_name", "tx_id", "tx_cds_seq_start", "tx_cds_seq_end", "exon_id")) # Extract one of the GRanges objects gr <- allTranscripts[[1]] # Check where in the transcript the fusion breakpoint hits decide_transcript_category(gr, fusion) # "exonBoundary" # Check another case gr <- allTranscripts[[3]] decide_transcript_category(gr, fusion) # "withinIntron"# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get all exons for all transcripts in the genes in the fusion transcript allTranscripts <- ensembldb::exonsBy( edb, filter = list( AnnotationFilter::GeneIdFilter( c( partner_gene_ensembl_id(upstream_partner_gene(fusion)), partner_gene_ensembl_id(downstream_partner_gene(fusion))))), columns = c( "gene_id", "gene_name", "tx_id", "tx_cds_seq_start", "tx_cds_seq_end", "exon_id")) # Extract one of the GRanges objects gr <- allTranscripts[[1]] # Check where in the transcript the fusion breakpoint hits decide_transcript_category(gr, fusion) # "exonBoundary" # Check another case gr <- allTranscripts[[3]] decide_transcript_category(gr, fusion) # "withinIntron"
This function takes a GRanges object and moves each IRanges object within next to each other starting at 1. This effectively removes the introns from the GRanges object.
down_shift(transcript)down_shift(transcript)
transcript |
The GRanges object to remove introns from. |
A GRanges object with introns removed.
# Create a simple GRanges object: gr <- IRanges::IRanges( start = c(13, 40, 100), end = c(20, 53, 110)) # Downshift it and see the introns are removed: down_shift(gr)# Create a simple GRanges object: gr <- IRanges::IRanges( start = c(13, 40, 100), end = c(20, 53, 110)) # Downshift it and see the introns are removed: down_shift(gr)
This getter retrieves the downstream PartnerGene object.
This sets the downstream PartnerGene object of a Fusion object
downstream_partner_gene(x) ## S4 method for signature 'Fusion' downstream_partner_gene(x) downstream_partner_gene(object) <- value ## S4 replacement method for signature 'Fusion' downstream_partner_gene(object) <- valuedownstream_partner_gene(x) ## S4 method for signature 'Fusion' downstream_partner_gene(x) downstream_partner_gene(object) <- value ## S4 replacement method for signature 'Fusion' downstream_partner_gene(object) <- value
x |
The Fusion object you wish to retrieve the downstream PartnerGene object for. |
object |
The Fusion object you wish to set a new downstream PartnerGene object for. |
value |
The new PartnerGene object. |
The downstream PartnerGene object.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the downstream fusion partner gene downstream_partner_gene(fusion) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the downstream PartnerGene object to be the same as the upstream # PartnerGene object downstream_partner_gene(fusion) <- upstream_partner_gene(fusion)# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the downstream fusion partner gene downstream_partner_gene(fusion) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the downstream PartnerGene object to be the same as the upstream # PartnerGene object downstream_partner_gene(fusion) <- upstream_partner_gene(fusion)
This function will fetch read sequences from fastq files and put them into new fastq files.
fetch_reads_from_fastq( reads, fastq_file_in1, fastq_file_in2, fastq_file_out1, fastq_file_out2 )fetch_reads_from_fastq( reads, fastq_file_in1, fastq_file_in2, fastq_file_out1, fastq_file_out2 )
reads |
List of read IDs that is to be fetched. |
fastq_file_in1 |
First fastq file to search in. |
fastq_file_in2 |
Second fastq file to seach in. |
fastq_file_out1 |
First fastq file with results. |
fastq_file_out2 |
Second fastq file with results. |
Note: This function runs (read only) bash commands on your system. Therefore the function will only work on a unix system.
The files fastqFileOut1 and fastqFileOut2 populated with the specified reads.
## Not run: # fastq files that has the supporting reads fastq1 <- system.file("extdata", "reads.1.fq", package="chimeraviz") fastq2 <- system.file("extdata", "reads.2.fq", package="chimeraviz") # Which read ids to extract reads <- c( "13422259", "19375605", "29755061", "31632876", "32141428", "33857245") # Extract the actual reads and put them in the tmp files "fastqFileOut1" and # "fastqFileOut2" fastqFileOut1 <- tempfile(pattern = "fq1", tmpdir = tempdir()) fastqFileOut2 <- tempfile(pattern = "fq2", tmpdir = tempdir()) fetch_reads_from_fastq(reads, fastq1, fastq2, fastqFileOut1, fastqFileOut2) # We now have the reads supporting fusion 5267 in the two files. ## End(Not run)## Not run: # fastq files that has the supporting reads fastq1 <- system.file("extdata", "reads.1.fq", package="chimeraviz") fastq2 <- system.file("extdata", "reads.2.fq", package="chimeraviz") # Which read ids to extract reads <- c( "13422259", "19375605", "29755061", "31632876", "32141428", "33857245") # Extract the actual reads and put them in the tmp files "fastqFileOut1" and # "fastqFileOut2" fastqFileOut1 <- tempfile(pattern = "fq1", tmpdir = tempdir()) fastqFileOut2 <- tempfile(pattern = "fq2", tmpdir = tempdir()) fetch_reads_from_fastq(reads, fastq1, fastq2, fastqFileOut1, fastqFileOut2) # We now have the reads supporting fusion 5267 in the two files. ## End(Not run)
This getter retrieves the spanning reads count from a Fusion object
fusion_spanning_reads_count(x) ## S4 method for signature 'Fusion' fusion_spanning_reads_count(x)fusion_spanning_reads_count(x) ## S4 method for signature 'Fusion' fusion_spanning_reads_count(x)
x |
The Fusion object you wish to retrieve the spanning reads count for. |
The Fusion spanning reads count.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the spanning reads count fusion_spanning_reads_count(fusion)# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the spanning reads count fusion_spanning_reads_count(fusion)
This getter retrieves the split reads count from a Fusion object
fusion_split_reads_count(x) ## S4 method for signature 'Fusion' fusion_split_reads_count(x)fusion_split_reads_count(x) ## S4 method for signature 'Fusion' fusion_split_reads_count(x)
x |
The Fusion object you wish to retrieve the split reads count for. |
The Fusion split reads count.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the split reads count fusion_split_reads_count(fusion)# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the split reads count fusion_split_reads_count(fusion)
This function is used in create_fusion_report() to convert Fusion objects to a data.frame-format.
fusion_to_data_frame(fusion)fusion_to_data_frame(fusion)
fusion |
The Fusion object to coerce. |
A data.frame with the fusion object.
create_fusion_report
# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) # Find the fusion object to create a data frame from fusion <- get_fusion_by_id(fusions, 5267) # Create the data frame dfFusion <- fusion_to_data_frame(fusion)# Load data defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) # Find the fusion object to create a data frame from fusion <- get_fusion_by_id(fusions, 5267) # Create the data frame dfFusion <- fusion_to_data_frame(fusion)
The Fusion class represents a fusion event, holding data imported from a fusion tool.
idA unique id representing a fusion event. For deFuse data this will be the cluster id.
fusion_toolName of the fusion tool.
genome_versionName of the genome used to map reads.
spanning_reads_countThe number of spanning reads supporting the fusion.
split_reads_countThe number of split reads supporting the fusion.
fusion_reads_alignmentA Gviz::AlignmentsTrack object holding the fusion reads aligned to the fusion sequence.
gene_upstreamA PartnerGene object holding information of the upstream fusion partner gene.
gene_downstreamA PartnerGene object holding information of the downstream fusion partner gene.
inframeA logical value indicating whether or not the downstream fusion partner gene is inframe or not. Not all fusion-finders report this.
fusion_tool_specific_dataA list that will hold fields of importance for a specific fusion finder. This field is used because many fusion-finders report important values that are hard to fit into a standardized format. Examples of values that are added to this list is probability from deFuse and EricScore from EricScript.
This function will get the ensembl ids from the org.Hs.eg.db/org.Mm.eg.db package given the gene names of the fusion event.
get_ensembl_ids(fusion)get_ensembl_ids(fusion)
fusion |
The Fusion object we want to get ensembl ids for. |
The Fusion object with Ensembl ids set.
# Import the filtered defuse results defuse833keFiltered <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833keFiltered, "hg19", 1) # Get a specific fusion fusion <- get_fusion_by_id(fusions, 5267) # See the ensembl ids: partner_gene_ensembl_id(upstream_partner_gene(fusion)) # [1] "ENSG00000180198" partner_gene_ensembl_id(downstream_partner_gene(fusion)) # [1] "ENSG00000162639" # Reset the fusion objects ensembl ids partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- "" partner_gene_ensembl_id(downstream_partner_gene(fusion)) <- "" # Get the ensembl ids fusion <- get_ensembl_ids(fusion) # See that we now have the same ensembl ids again: partner_gene_ensembl_id(upstream_partner_gene(fusion)) # [1] "ENSG00000180198" partner_gene_ensembl_id(downstream_partner_gene(fusion)) # [1] "ENSG00000162639"# Import the filtered defuse results defuse833keFiltered <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833keFiltered, "hg19", 1) # Get a specific fusion fusion <- get_fusion_by_id(fusions, 5267) # See the ensembl ids: partner_gene_ensembl_id(upstream_partner_gene(fusion)) # [1] "ENSG00000180198" partner_gene_ensembl_id(downstream_partner_gene(fusion)) # [1] "ENSG00000162639" # Reset the fusion objects ensembl ids partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- "" partner_gene_ensembl_id(downstream_partner_gene(fusion)) <- "" # Get the ensembl ids fusion <- get_ensembl_ids(fusion) # See that we now have the same ensembl ids again: partner_gene_ensembl_id(upstream_partner_gene(fusion)) # [1] "ENSG00000180198" partner_gene_ensembl_id(downstream_partner_gene(fusion)) # [1] "ENSG00000162639"
Helper function to retrieve the Fusion objects that involves genes in the given chromosome name.
get_fusion_by_chromosome(fusion_list, chr)get_fusion_by_chromosome(fusion_list, chr)
fusion_list |
A list of Fusion objects. |
chr |
The chromosome name we're looking for fusions in. |
A list of Fusion objects.
defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) length(get_fusion_by_chromosome(fusions, "chr1")) # [1] 1defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) length(get_fusion_by_chromosome(fusions, "chr1")) # [1] 1
Helper function to retrieve the Fusion objects that has geneName as one of the partner genes.
get_fusion_by_gene_name(fusion_list, gene_name)get_fusion_by_gene_name(fusion_list, gene_name)
fusion_list |
A list of Fusion objects. |
gene_name |
The gene name we're looking for. |
Note: get_fusion_by_gene_name(fusionList, "MT") will match both MT-ND5 and MT-ND4.
A list of Fusion objects.
defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) length(get_fusion_by_gene_name(fusions, "RCC1")) # [1] 1defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) length(get_fusion_by_gene_name(fusions, "RCC1")) # [1] 1
Helper function to retrieve the Fusion object with the given id.
get_fusion_by_id(fusion_list, id)get_fusion_by_id(fusion_list, id)
fusion_list |
A list of Fusion objects. |
id |
The id (e.g. the cluster_id from a deFuse run) we're looking for. |
A Fusion object.
defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # This should be the Fusion object: 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: +,-"defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # This should be the Fusion object: 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: +,-"
This function will retrieve transcripts for both genes in a fusion. It will check all transcripts and decide for each transcript if the fusion breakpoint happens at 1) an exon boundary, 2) within an exon, or 3) within an intron. This is done because fusions happening at exon boundaries are more likely to produce biologically interesting gene products. The function returns an updated Fusion object, where the fusion@gene_upstream@transcriptsX slots are set with transcript information.
get_transcripts_ensembl_db(fusion, edb)get_transcripts_ensembl_db(fusion, edb)
fusion |
The fusion object to find transcripts for. |
edb |
The edb object used to fetch data from. |
An updated fusion object with transcript data stored.
# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Add transcripts data to fusion object fusion <- get_transcripts_ensembl_db(fusion, edb) # The transcripts are now accessible through fusion@gene_upstream@transcripts and # fusion@gene_downstream@transcripts .# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Add transcripts data to fusion object fusion <- get_transcripts_ensembl_db(fusion, edb) # The transcripts are now accessible through fusion@gene_upstream@transcripts and # fusion@gene_downstream@transcripts .
A function that imports the results from an Aeron run into a list of Fusion objects.
import_aeron( filename_fusion_support, filename_fusion_transcript, genome_version, limit )import_aeron( filename_fusion_support, filename_fusion_transcript, genome_version, limit )
filename_fusion_support |
Filename for the Aeron result file fusion_support..txt. |
filename_fusion_transcript |
Filename for the Aeron result file fusion_transcripts..txt. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
Note that the strands and breakpoint positions are not included in the result files from Aeron. These have to be retrieved manually, using the ensembl identifiers (which are included in the result files, and will be available in the Fusion objects after importing).
A list of Fusion objects.
aeronfusionsupportfile <- system.file( "extdata", "aeron_fusion_support.txt", package="chimeraviz") aeronfusiontranscriptfile <- system.file( "extdata", "aeron_fusion_transcripts.fa", package="chimeraviz") fusions <- import_aeron( aeronfusionsupportfile, aeronfusiontranscriptfile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.aeronfusionsupportfile <- system.file( "extdata", "aeron_fusion_support.txt", package="chimeraviz") aeronfusiontranscriptfile <- system.file( "extdata", "aeron_fusion_transcripts.fa", package="chimeraviz") fusions <- import_aeron( aeronfusionsupportfile, aeronfusiontranscriptfile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a ChimPipe run, typically from a chimericJunctions_.txt file, into a list of Fusion objects.
import_chimpipe(filename, genome_version, limit)import_chimpipe(filename, genome_version, limit)
filename |
Filename for the ChimPipe results. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
chimpipefile <- system.file( "extdata", "chimericJunctions_MCF-7.txt", package="chimeraviz") fusions <- import_chimpipe(chimpipefile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.chimpipefile <- system.file( "extdata", "chimericJunctions_MCF-7.txt", package="chimeraviz") fusions <- import_chimpipe(chimpipefile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a deFuse run, typically from a results.filtered.tsv file, into a list of Fusion objects.
import_defuse(filename, genome_version, limit)import_defuse(filename, genome_version, limit)
filename |
Filename for the deFuse results .tsv file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a EricScript run into a list of Fusion objects.
import_ericscript(filename, genome_version, limit)import_ericscript(filename, genome_version, limit)
filename |
Filename for the EricScript results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
ericscriptData <- system.file( "extdata", "ericscript_SRR1657556.results.total.tsv", package = "chimeraviz") fusions <- import_ericscript(ericscriptData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.ericscriptData <- system.file( "extdata", "ericscript_SRR1657556.results.total.tsv", package = "chimeraviz") fusions <- import_ericscript(ericscriptData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
This alternative import function for use with Gviz::AlignmentsTrack imports a bamfile with non-UCSC chromosome names.
import_function_non_ucsc(file, selection)import_function_non_ucsc(file, selection)
file |
The bamfile. |
selection |
Which regions to get from the bamfile. |
A GRanges object with coverage data for the selection.
A function that imports the results from a Fusioncatcher run, typically from a final-list-candidate-fusion-genes.txt file, into a list of Fusion objects.
import_fusioncatcher(filename, genome_version, limit)import_fusioncatcher(filename, genome_version, limit)
filename |
Filename for the Fusioncatcher final-list-candidate-fusion-genes.txt results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
fusioncatcher833ke <- system.file( "extdata", "fusioncatcher_833ke_final-list-candidate-fusion-genes.txt", package = "chimeraviz") fusions <- import_fusioncatcher(fusioncatcher833ke, "hg38", 3) # This should import a list of 3 fusions described in Fusion objects.fusioncatcher833ke <- system.file( "extdata", "fusioncatcher_833ke_final-list-candidate-fusion-genes.txt", package = "chimeraviz") fusions <- import_fusioncatcher(fusioncatcher833ke, "hg38", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a FusionMap run, typically from a InputFastq.FusionReport.txt file, into a list of Fusion objects.
import_fusionmap(filename, genome_version, limit)import_fusionmap(filename, genome_version, limit)
filename |
Filename for the FusionMap PairedEndFusionReport.txt results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
fusionmapData <- system.file( "extdata", "FusionMap_01_TestDataset_InputFastq.FusionReport.txt", package = "chimeraviz") fusions <- import_fusionmap(fusionmapData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.fusionmapData <- system.file( "extdata", "FusionMap_01_TestDataset_InputFastq.FusionReport.txt", package = "chimeraviz") fusions <- import_fusionmap(fusionmapData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from an InFusion run nto a list of Fusion objects.
import_infusion(filename, genome_version, limit)import_infusion(filename, genome_version, limit)
filename |
Filename for the jaffa_results.csv file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
infusionData <- system.file( "extdata", "infusion_fusions.txt", package = "chimeraviz") fusions <- import_infusion(infusionData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.infusionData <- system.file( "extdata", "infusion_fusions.txt", package = "chimeraviz") fusions <- import_infusion(infusionData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a JAFFA run, typically from a jaffa_results.csv file, into a list of Fusion objects.
import_jaffa(filename, genome_version, limit)import_jaffa(filename, genome_version, limit)
filename |
Filename for the jaffa_results.csv file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
jaffaData <- system.file( "extdata", "jaffa_results.csv", package = "chimeraviz") fusions <- import_jaffa(jaffaData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.jaffaData <- system.file( "extdata", "jaffa_results.csv", package = "chimeraviz") fusions <- import_jaffa(jaffaData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a oncofuse run, typically from a results.filtered.tsv file, into a list of Fusion objects.
import_oncofuse(filename, genome_version, limit)import_oncofuse(filename, genome_version, limit)
filename |
Filename for the oncofuse results .tsv file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
This import function was contributed by Lavinia G, ref https://github.com/stianlagstad/chimeraviz/issues/47#issuecomment-409773158
A list of Fusion objects.
oncofuse833ke <- system.file( "extdata", "oncofuse.outfile", package="chimeraviz") fusions <- import_oncofuse(oncofuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.oncofuse833ke <- system.file( "extdata", "oncofuse.outfile", package="chimeraviz") fusions <- import_oncofuse(oncofuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a PRADA run into a list of Fusion objects.
import_prada(filename, genome_version, limit)import_prada(filename, genome_version, limit)
filename |
Filename for the PRADA results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
pradaData <- system.file( "extdata", "PRADA.acc.fusion.fq.TAF.tsv", package = "chimeraviz") fusions <- import_prada(pradaData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.pradaData <- system.file( "extdata", "PRADA.acc.fusion.fq.TAF.tsv", package = "chimeraviz") fusions <- import_prada(pradaData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a SOAPfuse run, typically from a final.Fusion.specific.for.genes file, into a list of Fusion objects.
import_soapfuse(filename, genome_version, limit)import_soapfuse(filename, genome_version, limit)
filename |
Filename for the SOAPfuse final-list-candidate-fusion-genes.txt results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
soapfuse833ke <- system.file( "extdata", "soapfuse_833ke_final.Fusion.specific.for.genes", package = "chimeraviz") fusions <- import_soapfuse(soapfuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.soapfuse833ke <- system.file( "extdata", "soapfuse_833ke_final.Fusion.specific.for.genes", package = "chimeraviz") fusions <- import_soapfuse(soapfuse833ke, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a SQUID run into a list of Fusion objects.
import_squid(filename, genome_version, limit)import_squid(filename, genome_version, limit)
filename |
Filename for the SQUID results. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
squidfile <- system.file( "extdata", "squid_hcc1954_sv.txt", package="chimeraviz") fusions <- import_squid(squidfile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.squidfile <- system.file( "extdata", "squid_hcc1954_sv.txt", package="chimeraviz") fusions <- import_squid(squidfile, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
A function that imports the results from a STAR-Fusion run, typically from a star-fusion.fusion_candidates.final.abridged file, into a list of Fusion objects.
import_starfusion(filename, genome_version, limit)import_starfusion(filename, genome_version, limit)
filename |
Filename for the STAR-Fusion star-fusion.fusion_candidates.final.abridged results file. |
genome_version |
Which genome was used in mapping (hg19, hg38, etc.). |
limit |
A limit on how many lines to read. |
A list of Fusion objects.
starfusionData <- system.file( "extdata", "star-fusion.fusion_candidates.final.abridged.txt", package = "chimeraviz") fusions <- import_starfusion(starfusionData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.starfusionData <- system.file( "extdata", "star-fusion.fusion_candidates.final.abridged.txt", package = "chimeraviz") fusions <- import_starfusion(starfusionData, "hg19", 3) # This should import a list of 3 fusions described in Fusion objects.
This getter retrieves the Ensembl ID from a PartnerGene object
This sets the Ensembl ID of a PartnerGene object.
partner_gene_ensembl_id(x) ## S4 method for signature 'PartnerGene' partner_gene_ensembl_id(x) partner_gene_ensembl_id(object) <- value ## S4 replacement method for signature 'PartnerGene' partner_gene_ensembl_id(object) <- valuepartner_gene_ensembl_id(x) ## S4 method for signature 'PartnerGene' partner_gene_ensembl_id(x) partner_gene_ensembl_id(object) <- value ## S4 replacement method for signature 'PartnerGene' partner_gene_ensembl_id(object) <- value
x |
The PartnerGene object you wish to retrieve the Ensembl ID for. |
object |
The PartnerGene object you wish to set a new Ensembl ID for. |
value |
The new Ensembl ID. |
The upstream fusion partner gene Ensembl ID.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the Ensembl ID from the upstream fusion partner gene partner_gene_ensembl_id(upstream_partner_gene(fusion)) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the downstream PartnerGene object to be the same as the upstream # PartnerGene object partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- "test"# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the Ensembl ID from the upstream fusion partner gene partner_gene_ensembl_id(upstream_partner_gene(fusion)) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the downstream PartnerGene object to be the same as the upstream # PartnerGene object partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- "test"
This getter retrieves the junction sequence from a PartnerGene object
partner_gene_junction_sequence(x) ## S4 method for signature 'PartnerGene' partner_gene_junction_sequence(x)partner_gene_junction_sequence(x) ## S4 method for signature 'PartnerGene' partner_gene_junction_sequence(x)
x |
The PartnerGene object you wish to retrieve the junction sequence for. |
The upstream fusion partner gene junction sequence.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the junction sequence from the upstream fusion partner gene partner_gene_junction_sequence(upstream_partner_gene(fusion))# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the junction sequence from the upstream fusion partner gene partner_gene_junction_sequence(upstream_partner_gene(fusion))
The PartnerGene class represents one of the genes in a fusion event.
nameCharacter containing name of the gene.
ensembl_idCharacter containing ensembl id for the gene.
chromosomeCharacter containing chromosome name.
breakpointNumeric containing the fusion breakpoint.
strandCharacter containing gene strand.
junction_sequenceBiostrings::DNAString containing the sequence right before/after the fusion breakpoint.
transcriptsGenomicRanges::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.
This function takes a list of Fusion objects and creates a circle plot indicating which chromosomes the fusion genes in the list consists of.
plot_circle(fusion_list)plot_circle(fusion_list)
fusion_list |
A list of Fusion objects. |
Note that only a limited number of gene names can be shown in the circle plot due to the limited resolution of the plot. RCircos will automatically limit the number of gene names shown if there are too many.
Creates a circle plot.
defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # Temporary file to store the plot pngFilename <- tempfile( pattern = "circlePlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_circle(fusions) # Close device dev.off()defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 3) # Temporary file to store the plot pngFilename <- tempfile( pattern = "circlePlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_circle(fusions) # Close device dev.off()
This function creates a plot with information about transcripts, coverage, location and more.
plot_fusion( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_separate( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_together( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL )plot_fusion( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_separate( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL ) plot_fusion_together( fusion, edb, bamfile = NULL, which_transcripts = "exonBoundary", ylim = c(0, 1000), non_ucsc = TRUE, reduce_transcripts = FALSE, bedgraphfile = NULL )
fusion |
The Fusion object to plot. |
edb |
The ensembldb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
ylim |
Limits for the coverage y-axis. |
non_ucsc |
Boolean indicating whether or not the bamfile used has UCSC- styled chromosome names (i.e. with the "chr" prefix). Setting this to true lets you use a bamfile with chromosome names like "1" and "X", instead of "chr1" and "chrX". |
reduce_transcripts |
Boolean indicating whether or not to reduce all transcripts into a single transcript for each partner gene. |
bedgraphfile |
A bedGraph file to use instead of the bamfile to plot coverage. |
plot_fusion() will dispatch to either plot_fusion_separate() or plot_fusion_together(). plot_fusion_separate() will plot the fusion gene partners in separate graphs shown next to each other, while plot_fusion_together() will plot the fusion gene partners in the same graph with the same x-axis. plot_fusion() will dispatch to plot_fusion_together() if the fusion gene partners are on the same strand, same chromosome and are close together (<=50,000 bp apart).
Creates a fusion plot.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bamfile = bamfile5267, edb = edb, non_ucsc = TRUE) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bedgraphfile = bedgraphfile, edb = edb, non_ucsc = TRUE) # Close device dev.off()# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bamfile = bamfile5267, edb = edb, non_ucsc = TRUE) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 1000, height = 750) # Plot! plot_fusion( fusion = fusion, bedgraphfile = bedgraphfile, edb = edb, non_ucsc = TRUE) # Close device dev.off()
This function takes a Fusion object and plots the reads supporting the fusion on top of the fusion sequence (fusion@junction_sequence), provided that add_fusion_reads_alignment() has been run earlier in order to add fusion reads alignment data to the fusion object.
plot_fusion_reads(fusion, show_all_nucleotides = TRUE, nucleotide_amount = 10)plot_fusion_reads(fusion, show_all_nucleotides = TRUE, nucleotide_amount = 10)
fusion |
The Fusion object to plot. |
show_all_nucleotides |
Boolean indicating whether or not to show all nucleotides. If FALSE, then only nucleotide_amount amount of nucleotides will be shown on each end of the fusion junction. If TRUE, then the whole fusion junction sequence will be shown. |
nucleotide_amount |
The number of nucleotides to show on each end of the fusion junction sequence. Defaults to 10. Only applicable if show_all_nucleotides is set to TRUE. |
Note that the package used for plotting, Gviz, is strict on chromosome names. If the plot produced doesn't show the reads, the problem might be solved by naming the fusion sequence "chrNA".
Creates a fusion reads plot.
add_fusion_reads_alignment
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) # Find the specific fusion we have aligned reads for fusion <- get_fusion_by_id(fusions, 5267) bamfile <- system.file( "extdata", "5267readsAligned.bam", package="chimeraviz") # Add the bam file of aligned fusion reads to the fusion object fusion <- add_fusion_reads_alignment(fusion, bamfile) # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Calculate image size based on supporting reads and lenght of junction # sequence. imageWidth <- (nchar(partner_gene_junction_sequence(upstream_partner_gene(fusion))) + nchar(partner_gene_junction_sequence(downstream_partner_gene(fusion)))) * 15 imageHeight <- (fusion_split_reads_count(fusion)+fusion_spanning_reads_count(fusion)) * 20 # Open device png(pngFilename, width = imageWidth, height = imageHeight) # Now we can plot plot_fusion_reads(fusion) # Close device dev.off()# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) # Find the specific fusion we have aligned reads for fusion <- get_fusion_by_id(fusions, 5267) bamfile <- system.file( "extdata", "5267readsAligned.bam", package="chimeraviz") # Add the bam file of aligned fusion reads to the fusion object fusion <- add_fusion_reads_alignment(fusion, bamfile) # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Calculate image size based on supporting reads and lenght of junction # sequence. imageWidth <- (nchar(partner_gene_junction_sequence(upstream_partner_gene(fusion))) + nchar(partner_gene_junction_sequence(downstream_partner_gene(fusion)))) * 15 imageHeight <- (fusion_split_reads_count(fusion)+fusion_spanning_reads_count(fusion)) * 20 # Open device png(pngFilename, width = imageWidth, height = imageHeight) # Now we can plot plot_fusion_reads(fusion) # Close device dev.off()
This function takes a fusion object and an ensembldb object and plots the reduced version of the fusion transcript. This transcript consist of the "mashed together" version of all possible fusion transcripts based on known annotations. If a bamfile is specified, the fusion transcript will be plotted with coverage information.
plot_fusion_transcript( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", bedgraphfile = NULL )plot_fusion_transcript( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", bedgraphfile = NULL )
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
bedgraphfile |
A bedGraph file to use instead of the bamfile to plot coverage. |
Note that the transcript database used (the edb object) must have the same seqnames as any bamfile used. Otherwise the coverage data will be wrong.
Creates a fusion transcript plot.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript( fusion = fusion, bamfile = bamfile5267, edb = edb) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript( fusion = fusion, bamfile = bamfile5267, edb = edb) # Close device dev.off()# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript( fusion = fusion, bamfile = bamfile5267, edb = edb) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript( fusion = fusion, bamfile = bamfile5267, edb = edb) # Close device dev.off()
This function takes a fusion object, an ensembldb object, a bedfile with protein domain data and two specific transcript ids. The function plots the specific fusion transcript along with annotations of protein domains. If a bamfile is specified, the fusion transcript will be plotted with coverage information.
plot_fusion_transcript_with_protein_domain( fusion, edb = NULL, bamfile = NULL, bedfile = NULL, gene_upstream_transcript = "", gene_downstream_transcript = "", plot_downstream_protein_domains_if_fusion_is_out_of_frame = FALSE )plot_fusion_transcript_with_protein_domain( fusion, edb = NULL, bamfile = NULL, bedfile = NULL, gene_upstream_transcript = "", gene_downstream_transcript = "", plot_downstream_protein_domains_if_fusion_is_out_of_frame = FALSE )
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
bedfile |
The bedfile with protein domain data. |
gene_upstream_transcript |
The transcript id for the upstream gene. |
gene_downstream_transcript |
The transcript id for the downstream gene. |
plot_downstream_protein_domains_if_fusion_is_out_of_frame |
Setting this to true makes the function plot protein domains in the downstream gene even though the fusion is out of frame. |
Note that the transcript database used (the edb object) must have the same seqnames as any bamfile used. Otherwise the coverage data will be wrong.
Creates a fusion transcript plot with annotations of protein domains.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Select transcripts gene_upstream_transcript <- "ENST00000434290" gene_downstream_transcript <- "ENST00000370031" # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # bedfile with protein domains for the transcripts in this example bedfile <- system.file( "extdata", "protein_domains_5267.bed", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript_with_protein_domain( fusion = fusion, edb = edb, bamfile = bamfile5267, bedfile = bedfile, gene_upstream_transcript = gene_upstream_transcript, gene_downstream_transcript = gene_downstream_transcript, plot_downstream_protein_domains_if_fusion_is_out_of_frame = TRUE) # Close device dev.off()# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Select transcripts gene_upstream_transcript <- "ENST00000434290" gene_downstream_transcript <- "ENST00000370031" # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # bedfile with protein domains for the transcripts in this example bedfile <- system.file( "extdata", "protein_domains_5267.bed", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcript_with_protein_domain( fusion = fusion, edb = edb, bamfile = bamfile5267, bedfile = bedfile, gene_upstream_transcript = gene_upstream_transcript, gene_downstream_transcript = gene_downstream_transcript, plot_downstream_protein_domains_if_fusion_is_out_of_frame = TRUE) # Close device dev.off()
This function takes a fusion object and a TranscriptDb object and plots a graph showing the possible fusion transcripts.
plot_fusion_transcripts_graph( fusion, edb = NULL, which_transcripts = "exonBoundary", rankdir = "TB" )plot_fusion_transcripts_graph( fusion, edb = NULL, which_transcripts = "exonBoundary", rankdir = "TB" )
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch data. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
rankdir |
Choose whether the graph should be plotted from left to right ("LR"), or from top to bottom ("TB"). This parameter is given to Rgraphviz::plot(). |
Creates a fusion transcripts graph plot.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcripts_graph( fusion = fusion, edb = edb) # Close device dev.off()# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_fusion_transcripts_graph( fusion = fusion, edb = edb) # Close device dev.off()
This function takes a fusion object and an ensembldb object and plots transcripts for both genes, showing which parts of each genes are included in the fusion event. If the bamfile parameter is set, then the coverage is plotted beneath the transcripts.
plot_transcripts( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", non_ucsc = TRUE, ylim = c(0, 1000), reduce_transcripts = FALSE, bedgraphfile = NULL )plot_transcripts( fusion, edb = NULL, bamfile = NULL, which_transcripts = "exonBoundary", non_ucsc = TRUE, ylim = c(0, 1000), reduce_transcripts = FALSE, bedgraphfile = NULL )
fusion |
The Fusion object to plot. |
edb |
The edb object that will be used to fetch data. |
bamfile |
The bamfile with RNA-seq data. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
non_ucsc |
Boolean indicating whether or not the bamfile used has UCSC- styled chromosome names (i.e. with the "chr" prefix). Setting this to true lets you use a bamfile with chromosome names like "1" and "X", instead of "chr1" and "chrX". |
ylim |
Limits for the coverage y-axis. |
reduce_transcripts |
Boolean indicating whether or not to reduce all transcripts into a single transcript for each partner gene. |
bedgraphfile |
A bedGraph file to use instead of the bamfile to plot coverage. |
Creates a fusion transcripts plot.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_transcripts( fusion = fusion, edb = edb, bamfile = bamfile5267, non_ucsc = TRUE) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_transcripts( fusion = fusion, edb = edb, bedgraphfile = bedgraphfile, non_ucsc = TRUE) # Close device dev.off()# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bamfile with reads in the regions of this fusion event bamfile5267 <- system.file( "extdata", "fusion5267and11759reads.bam", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_transcripts( fusion = fusion, edb = edb, bamfile = bamfile5267, non_ucsc = TRUE) # Close device dev.off() # Example using a .bedGraph file instead of a .bam file: # Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # bedgraphfile with coverage data from the regions of this fusion event bedgraphfile <- system.file( "extdata", "fusion5267and11759reads.bedGraph", package="chimeraviz") # Temporary file to store the plot pngFilename <- tempfile( pattern = "fusionPlot", fileext = ".png", tmpdir = tempdir()) # Open device png(pngFilename, width = 500, height = 500) # Plot! plot_transcripts( fusion = fusion, edb = edb, bedgraphfile = bedgraphfile, non_ucsc = TRUE) # Close device dev.off()
Documentation for the ChimPipe example data.
Documentation for the SQUID example data.
This is example data from the ChimPipe tutorial all-in-one package located at https://chimpipe.readthedocs.io/en/latest/tutorial.html#download-all-in-one-package It was downloaded March 10th 2020
This is example data for SQUID provided on GitHub here: https://github.com/Kingsford-Group/squid/issues/20#issuecomment-598888472 It was downloaded March 17th 2020
Cytoband information for the HG19 assembly from UCSC. Downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/
This data is used with RCircos in plot_circle().
Cytoband information for the HG38 assembly from UCSC. Downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg38database/
All _alt or _random entries has been manually removed, as has the chrM entry.
This data is used with RCircos in plot_circle().
Documentation for the deFuse example data.
This file has the results from a run of deFuse-0.7.0 on the 833ke cell line. The program was ran with the standard configuration, but with the parameter span_count_threshold=5 instead of the standard 3. The resulting results.filtered.tsv file was then manually filtered to only include 17 fusion events in the interest of saving computing time for tests and examples. The original results contained 171 fusion events.
These two files, reads_supporting_defuse_fusion_5267.1.fq and reads_supporting_defuse_fusion_5267.2.fq, contains the reads that support the fusion event with cluster_id 5267.
The bamfile 5267readsAligned.bam and the 5267readsAligned.bam.bai index file contains the reads supporting the fusion event with cluster_id 5267 aligned to the fusion sequence. It is used with plot_fusion_reads().
Documentation for the EricScript example data.
This is example data thankfully provided by EricScript author Matteo Benelli.
Documentation for the protein_domains_5267.bed file containing protein domains for the genes in the fusion with cluster_id=5267.
This file is an excerpt from a larger file that we created by: - downloading domain name annotation from Pfam database (PfamA version 31) and domain region annotation from Ensembl database through BioMart API - switching the domain coordinates in the protein level to these in transcript level.
Documentation for the fusion5267and11759reads.bam file containing reads mapped to the region where the genes in the fusions with cluster_id=5267 and cluster_id=11759 is.
This file is the result of running these commands:
samtools view -b original_bamfile.bam "1:28831455-28866812" "1:109189912-109205148" "12:8608225-8677832" > fusion5267and11759reads.bam samtools index fusion5267and11759reads.bam fusion5267and11759reads.bam.bai
where we extract the reads mapping to the region where we know the fusions with cluster_id=5267 and cluster_id=11759 from the deFuse example data is.
The original_bamfile.bam is from a study of the 833KE cell line by Andreas M. Hoff et al., documented in the paper [Identification of Novel Fusion Genes in Testicular Germ Cell Tumors](http://cancerres.aacrjournals.org/content/76/1/108.full).
Documentation for the fusion5267and11759reads.bedGraph file containing read count data from the regions of the fusion event with cluster_id=5267.
This file is the result of running this command:
bedtools genomecov -ibam fusion5267and11759reads.bam -bg > fusion5267and11759reads.bam.bedGraph
fusion5267and11759reads.bam has its own documentation entry for how it was created.
Documentation for the Fusioncatcher example data.
This file has the results from a run of Fusioncatcher-0.99.3e on the 833ke cell line. The program was ran with the standard configuration file and with the parameters "-p 8 -z –keep-preliminary".
Documentation for the FusionMap example data.
This is example data provided with the FusionMap version released 2015-03-31.
Homo_sapiens.GRCh37.74_subset.gtf
The Homo_sapiens.GRCh37.74.gtf file is a subset version of the Ensembl Homo_sapiens.GRCh37.74.gtf file, located here: ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens. This gtf file contains transcripts for the partner genes in two of the fusion transcripts from the deFuse example data provided with this package: The fusion transcript with cluster_id=5267, and the fusion transcript with cluster_id=11759.
The file is the result of running this command:
# grep "ENST00000373831\|ENST00000373832\|ENST00000373833\|ENST00000398958\|ENST00000411533\|ENST00000419074\|ENST00000427469\|ENST00000429051\|ENST00000430407\|ENST00000434290\|ENST00000478232\|ENST00000486790\|ENST00000370031\|ENST00000370032\|ENST00000402983\|ENST00000420055\|ENST00000483729\|ENST00000493676\|ENST00000382073\|ENST00000299665\|ENST00000382064" Homo_sapiens.GRCh37.74.gtf > Homo_sapiens.GRCh37.74_subset.gtf
The transcript names given in the command above are all transcripts available for the genes CLEC6A, CLEC4D, HENMT1, and RCC1 in Ensembl version 74.
The Homo_sapiens.GRCh37.74.sqlite file is the sqlite database that the Ensembldb package creates from the corresponding gtf file. It was created using this command:
# ensDbFromGtf( # gtf = "Homo_sapiens.GRCh37.74_subset.gtf", # organism = "Homo_sapiens", # genomeVersion = "GRCh37", # version = 74)
Documentation for the InFusion example data.
This is example data from the InFusion getting started page located at https://bitbucket.org/kokonech/infusion/wiki/Getting
Documentation for the JAFFA example data.
This is example data from the described JAFFA example run documented at https://github.com/Oshlack/JAFFA/wiki/Example .
Documentation for the oncofuse example data.
The example output from oncofuse was kindly provided by Lavinia G here: https://github.com/stianlagstad/chimeraviz/issues/47#issuecomment-409773158
Documentation for the PRADA example data.
This is example data thankfully provided by PRADA authors Siyuan Zheng and Roeland Verhaak.
Documentation for the SOAPfuse example data.
This file has the results from a run of soapfuse-1.26 on the 833ke cell line. The program was ran with the standard configuration file.
Documentation for the STAR-Fusion example data.
This example data was retrieved from the STAR-Fusion github page June 2.nd 2017.
This function takes a GenePartner object and creates a transcript data.frame with transcript information, including only the transcripts given by the parameter which_transcripts
select_transcript(gene_partner, which_transcripts = "exonBoundary")select_transcript(gene_partner, which_transcripts = "exonBoundary")
gene_partner |
The GenePartner object to select a transcript for. |
which_transcripts |
This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary". |
select_transcript() selects which transcript to create by this prioritization:
1. Exon boundary transcripts. 2. Within exon transcripts. 3. Within intron transcripts. 4. Intergenic transcripts.
A data.frame with transcript data.
# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get transcripts fusion <- get_transcripts_ensembl_db(fusion, edb) # Select transcript transcriptsA <- select_transcript(upstream_partner_gene(fusion))# Load data and example fusion event defuse833ke <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833ke, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Load edb edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get transcripts fusion <- get_transcripts_ensembl_db(fusion, edb) # Select transcript transcriptsA <- select_transcript(upstream_partner_gene(fusion))
Show method for the Fusion class.
## S4 method for signature 'Fusion' show(object)## S4 method for signature 'Fusion' show(object)
object |
A Fusion object |
Shows information about a Fusion object.
Show method for the PartnerGene class.
## S4 method for signature 'PartnerGene' show(object)## S4 method for signature 'PartnerGene' show(object)
object |
A PartnerGene object |
Shows information about a PartnerGene object.
This function will look for ranges (exons) in the GRanges object that has the coding DNA sequence starting or stopping within it. If found, these exons are split, and each exon in the GRanges object will be tagged as either "protein_coding", "5utr", or "3utr". The returned GRanges object will have feature values set in mcols(gr)$feature reflecting this.
split_on_utr_and_add_feature(gr)split_on_utr_and_add_feature(gr)
gr |
The GRanges object we want to split and tag with feature info. |
An updated GRanges object with feature values set.
# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get all exons for all transcripts in the genes in the fusion transcript allTranscripts <- ensembldb::exonsBy( edb, filter = list( AnnotationFilter::GeneIdFilter( c( partner_gene_ensembl_id(upstream_partner_gene(fusion)), partner_gene_ensembl_id(downstream_partner_gene(fusion))))), columns = c( "gene_id", "gene_name", "tx_id", "tx_cds_seq_start", "tx_cds_seq_end", "exon_id")) # Extract one of the GRanges objects gr <- allTranscripts[[1]] # Check how many ranges there are here length(gr) # Should be 9 ranges # Split the ranges containing the cds start/stop positions and add feature # values: gr <- split_on_utr_and_add_feature(gr) # Check the length again length(gr) # Should be 11 now, as the range containing the cds_strat position and the # range containing the cds_stop position has been split into separate ranges# Load fusion data and choose a fusion object: defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- get_fusion_by_id(fusions, 5267) # Create edb object edbSqliteFile <- system.file( "extdata", "Homo_sapiens.GRCh37.74.sqlite", package="chimeraviz") edb <- ensembldb::EnsDb(edbSqliteFile) # Get all exons for all transcripts in the genes in the fusion transcript allTranscripts <- ensembldb::exonsBy( edb, filter = list( AnnotationFilter::GeneIdFilter( c( partner_gene_ensembl_id(upstream_partner_gene(fusion)), partner_gene_ensembl_id(downstream_partner_gene(fusion))))), columns = c( "gene_id", "gene_name", "tx_id", "tx_cds_seq_start", "tx_cds_seq_end", "exon_id")) # Extract one of the GRanges objects gr <- allTranscripts[[1]] # Check how many ranges there are here length(gr) # Should be 9 ranges # Split the ranges containing the cds start/stop positions and add feature # values: gr <- split_on_utr_and_add_feature(gr) # Check the length again length(gr) # Should be 11 now, as the range containing the cds_strat position and the # range containing the cds_stop position has been split into separate ranges
This getter retrieves the upstream PartnerGene object.
This sets the upstream PartnerGene object of a Fusion object
upstream_partner_gene(x) ## S4 method for signature 'Fusion' upstream_partner_gene(x) upstream_partner_gene(object) <- value ## S4 replacement method for signature 'Fusion' upstream_partner_gene(object) <- valueupstream_partner_gene(x) ## S4 method for signature 'Fusion' upstream_partner_gene(x) upstream_partner_gene(object) <- value ## S4 replacement method for signature 'Fusion' upstream_partner_gene(object) <- value
x |
The Fusion object you wish to retrieve the upstream PartnerGene object for. |
object |
The Fusion object you wish to set a new upstream PartnerGene object for. |
value |
The new PartnerGene object. |
The upstream PartnerGene object.
# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the upstream fusion partner gene upstream_partner_gene(fusion) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the upstream PartnerGene object to be the same as the downstream # PartnerGene object upstream_partner_gene(fusion) <- downstream_partner_gene(fusion)# Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Get the upstream fusion partner gene upstream_partner_gene(fusion) # Load data defuseData <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuseData, "hg19", 1) fusion <- fusions[[1]] # Set the upstream PartnerGene object to be the same as the downstream # PartnerGene object upstream_partner_gene(fusion) <- downstream_partner_gene(fusion)
This function will write the fusion sequence to a fasta file, using Biostring::writeXStringSet() .
write_fusion_reference(fusion, filename)write_fusion_reference(fusion, filename)
fusion |
The Fusion object we want to create a fasta file from. |
filename |
The filename to write to. |
Writes the fusion junction sequence to the given filename.
# Import the filtered defuse results defuse833keFiltered <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833keFiltered, "hg19", 1) # Get a specific fusion fusion <- get_fusion_by_id(fusions, 5267) # Create temporary file to hold the fusion sequence fastaFileOut <- tempfile(pattern = "fusionSequence", tmpdir = tempdir()) # Write fusion sequence to file write_fusion_reference(fusion, fastaFileOut)# Import the filtered defuse results defuse833keFiltered <- system.file( "extdata", "defuse_833ke_results.filtered.tsv", package="chimeraviz") fusions <- import_defuse(defuse833keFiltered, "hg19", 1) # Get a specific fusion fusion <- get_fusion_by_id(fusions, 5267) # Create temporary file to hold the fusion sequence fastaFileOut <- tempfile(pattern = "fusionSequence", tmpdir = tempdir()) # Write fusion sequence to file write_fusion_reference(fusion, fastaFileOut)