This is class representation for a fusion event.
A list: fusionTool: the tool that has generated the fusions UniqueCuttingPositionCount: the number of unique cutting positions detected for the fusion. SeedCount: the number of reads overlapping the break-point, i.e. spanning reads (FusionMap, FusionHunter, mapSplice, Tophat-fusion, ChimeraScan, STAR, Rsubread, FusionCatcher). Both spanning and encompassing reads (Bellerophontes, FusionFinder). Encompassing reads, i.e. one read of a pair on gene 1, and the other on gene2 (deFuse). RescuedCount: the number of reads overlapping the break-point rescued after identification of the break point (FusionMap). Encompassing reads (Tophat-fusionm Tophat-fusion-post, FusionCatcher, STAR). Both spanning and encompassing reads (ChimeraScan, Rsubread). SplicePattern: the splice pattern for a fusion junction FusionGene: the name of the fusion gene in the format gene1 -> gene2. frameShift: frameshift at break-point
A GRangesList encompassing fusion locations for gene 1 and 2
A DNAStringSet encompassing the fusion transcript that can be generated by chimeraSeqs function.
A GAlignments object encompassing positions for all reads mapping on the DNAStringSet located in fusionRNA slot
Standard generic methods:
An accessor function used to retrieve information for a fusion
An accessor function used to retrieve GRangesList encompassing fusion locations for gene 1 and 2
An accessor function used to extract the DNAStringSet
An accessor function used to add the DNAStringSet to the fset object
An accessor function used to extract the GAlignments object
An accessor function used to add the GAlignments object to the fSet object
newfSet(fusionInfo = list(),
fusionLoc = GRangesList(),
fusionRNA = DNAStringSet(),
fusionGA = GAlignments()):
Creates a fSet object.
A list of the fusin characteristics see above slot fusionInfo
A GRangesList encompassing the fusion break points
A DNAStringSet encompassing the fusion transcript
A GAlignments encompassing the location of reads mapping on the fusion transcript
Raffaele A Calogero
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#creating a fusion report from output of fusionMap tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19") #extracting the fusions names fusion.names <- fusionName(tmp) fusion.names #extracting the fSet object ofr one of the fusions myset <- tmp[] #constructing the fused sequence(s) trs <- chimeraSeqs(myset, type="transcripts") #adding the sequences to the fSet object myset <- addRNA(myset , trs) #extracting sequences from an fSet object tmp.seq <- fusionRNA(myset) #adding reads mapped on the fusion generated using tophatRun function myset <- addGA(myset, paste(path.package(package="chimera"),"/examples/mcf7_trs_accepted_hits.bam",sep="")) #extracting the GAlignments from an fSet object ga <- fusionGA(myset)
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