class.fSet: Class fSet, a class represent fusion data, and methods for...
In chimera: A package for secondary analysis of fusion products

Description Slots Methods Constructor Author(s) See Also Examples

This is class representation for a fusion event.

fusionInfo: 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
fusionLoc: A GRangesList encompassing fusion locations for gene 1 and 2
fusionRNA: A DNAStringSet encompassing the fusion transcript that can be generated by chimeraSeqs function.
fusionGA: A GAlignments object encompassing positions for all reads mapping on the DNAStringSet located in fusionRNA slot

Standard generic methods:

fusionData(fSet): An accessor function used to retrieve information for a fusion
fusionGRL(fSet): An accessor function used to retrieve GRangesList encompassing fusion locations for gene 1 and 2
fusionRNA(fSet): An accessor function used to extract the DNAStringSet
addRNA(fSet, rna): An accessor function used to add the DNAStringSet to the fset object
fusionGA(fSet): An accessor function used to extract the GAlignments object
addGA(fSet, bam): An accessor function used to add the GAlignments object to the fSet object

newfSet

newfSet(fusionInfo = list(), fusionLoc = GRangesList(), fusionRNA = DNAStringSet(), fusionGA = GAlignments()): Creates a fSet object.

fusionInfo: A list of the fusin characteristics see above slot fusionInfo
fusionLoc: A GRangesList encompassing the fusion break points
fusionRNA: A DNAStringSet encompassing the fusion transcript
fusionGA: A GAlignments encompassing the location of reads mapping on the fusion transcript

Raffaele A Calogero

chimeraSeqs, oncofuseRun, fusionPeptides, prettyPrint

#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[[13]]
#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)