fSet {chimera} | R Documentation

## Class fSet, a class represent fusion data, and methods for processing it

### Description

This is class representation for a fusion event.

### Slots

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

### Methods

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

### Constructor

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

### Author(s)

Raffaele A Calogero

### See Also

`chimeraSeqs`, `oncofuseRun`, `fusionPeptides`, `prettyPrint`

### Examples

    #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)

[Package chimera version 1.22.0 Index]