df.e: Example data

In yhoogstrate/FuMaR: FusionMatcher (R wrapper)

Usage

data("df.e")

Format

The format is: List of 915 $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "11" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND5->J01415.25" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 13868 8407 .. .. .. .. .. .. .. ..@ width : int [1:2] 139 153 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND5" "J01415.25" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTA"| __truncated__ "CCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "99" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND4->MT-ND2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 11483 5320 .. .. .. .. .. .. .. ..@ width : int [1:2] 224 66 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND4" "MT-ND2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATC"| __truncated__ "CCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "SCNN1A->TNFRSF1A" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 6457765 6443410 .. .. .. .. .. .. .. ..@ width : int [1:2] 129 117 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "SCNN1A" "TNFRSF1A" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGGGTCTTCCAGATGCTATCGCGACAGAACAATTACACCGTCAACAACAAGAGAAATGGAGTGGCCAAAGTCAACATCTTCTTCAAGGAGCTGAACTACAAAACCAATTCTGAGTCTCCCTCTGTCA"| __truncated__ "GGTGCTCCTGGAGCTGTTGGTGGGAATATACCCCTCAGGGGTTATTGGACTGGTCCCTCACCTAGGGGACAGGGAGAAGAGAGATAGTGTGTGTCCCCAAGGAAAATATATCCACC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "4" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "HGSNAT->RP11-428L9.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr8","chr10": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 43035429 8925081 .. .. .. .. .. .. .. ..@ width : int [1:2] 123 93 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "HGSNAT" "RP11-428L9.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCACCTCTGCCCCGCCGCCCTGTCTGGGATGTGAGGAGTGCCTCTGCTGGGCCGCAGCCCTGTCTGGGAG" "AAAGAAGGTGATTAATTCTGCCTAAGTTCGACACGATCCCATGAGACGACCCTGCCATCCAGAGAAGCACAATCTTCAGCCTTCAAGACACT" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr8" "chr10" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "1539" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "J01415.2->MT-CO2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 144 7686 .. .. .. .. .. .. .. ..@ width : int [1:2] 200 262 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "J01415.2" "MT-CO2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCAC"| __truncated__ "TCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCAT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "411" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AL445074.1->HFM1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr14","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 43722980 91853147 .. .. .. .. .. .. .. ..@ width : int [1:2] 34 174 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AL445074.1" "HFM1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AAATCTCAAAGGTTCTTTTTTCACTGACCCGGT" "CCGGGGACAGTGCCAGGTGGGGAGTTTGACTGGGGCTGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAAAAGCTCGCTT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr14" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "10" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "HSP90AA1->CTB-161M19.3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr14","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 102550712 118309569 .. .. .. .. .. .. .. ..@ width : int [1:2] 327 188 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "HSP90AA1" "CTB-161M19.3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTTTATTGGATATCCCATTACTCTTTTTGTGGAGAAGGAACGTGATAAAGAAGTAAGCGATGATGAGGCTGAAGAAAAGGAAGACAAAGAAGAAGAAAAAGAAAAAGAAGAGAAAGAGTCGGAAGAC"| __truncated__ "GCAGAAAATGGAAGAGACGCCCCTGCTAACGGGAATGCTAATGAGGAAAATGGGGAGCAGGAGGCTGACAATGAGGTAGATGAAGAAGAGGAAGAAGGTGGGGAGGAAGAGGAGGAGGAAGAAGGTG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr14" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "12" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "KRT7->KRT8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 52628783 53298489 .. .. .. .. .. .. .. ..@ width : int [1:2] 172 243 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "KRT7" "KRT8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCCCGGTGGGCGCCGGCATCCGCGAGGTCACCATTAACCAGAGCCTGCTGGCCCCGCTGCGGCTGGACGCCGACCCCTCCCTCCAGCGGGTGCGCCAGGAGGAGAGCGAGCAGATCAAGACCCTCAA"| __truncated__ "GAGCAGATCAAGACCCTCAACAACAAGTTTGCCTCCTTCATAGACAAGGTACGGTTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCTCCTGCAGCAGCAGAAGACGGCTCGAAGCA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "6" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CDK12->U6.891" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr17": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 37682443 37700499 .. .. .. .. .. .. .. ..@ width : int [1:2] 124 113 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CDK12" "U6.891" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTCTCTTGAGTCAGCTGATGAAAACCCAAGAGCCAGCAGGCAGTCTGGAGGAAAACAACAGTGACAAGAACAGTGGGCCACAGGGGCCCCGAAGAACTCCCACAATGCCACAGGAGGAGGCAG" "CAGGTAGGAGCAACGGTGGGAATGCCCTCTGAGGAATGCAGTGATGTCCATCAGTCACCTCTCACCCAGAGCCTGGCAAATTCAGTCTCTTTCACAGAACCTAAAGCCAAGC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr17" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "37062" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "UNC45B->RN28S1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chrX": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 33477961 108297810 .. .. .. .. .. .. .. ..@ width : int [1:2] 156 91 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "UNC45B" "RN28S1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTTGTCAGCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAATGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCCGCCCCG"| __truncated__ "GAAGCGAGAGCCCCTCAGGGCTCGCCCCCCCGCCTCACCGGGTCAGTGAAAAAACGATCAGAGTAGTGGTATTTCACCGGCGGCCCGCAG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chrX" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "3" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AC021860.1->RAB11B" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr4","chr19": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 38637401 8451051 .. .. .. .. .. .. .. ..@ width : int [1:2] 196 144 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AC021860.1" "RAB11B" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACACTGCCTTTAAGAACTGTAACACTCACCGCGAGGGTCCGCAGCTTCATTCTTGAAGTCAGTGAGACCAAGAACCCACCAATTCCGGACACACATAGCAGGAGGACACAGGACTGAAACATGTATT"| __truncated__ "CGAGGCCATCAAGCTACAGATGGTCTTAAAAATGGAACCCCAAATGAGTTCAACTAACAACTTCTACTGAGGACCCCTGGACCGACCCACTGGCCCTTCCACTGGCCTAAAGAGTTCCCCTCTGGAG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr4" "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "3847" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "5_8S_rRNA.2->AL357561.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr16","chr6": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 33964009 150665062 .. .. .. .. .. .. .. ..@ width : int [1:2] 124 154 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "5_8S_rRNA.2" "AL357561.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTCCGGGACTGCACGCGCGCTACACTGACTGGCTCAGCGTGTGCCTACCCTACGTGGCAGAGGCGGGTAACCTGTTGAACCTCATTCGTGATGGGGATGGGGGATTGCAATTATTCCCCATGA" "ACTGAGGGTGGCAAGAGGAAGGAAAAACAGACAGAAGTAAATGGAAAAACAGAATTCAGTTGACTCATTTTTGCCTTTGGCTAAATAAAGTAGTCTATGGCTCCTACTGATTGGATGGTTTAGTGAG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr16" "chr6" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "FASN->KIAA1432" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr9": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 80048997 5684298 .. .. .. .. .. .. .. ..@ width : int [1:2] 215 33 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "FASN" "KIAA1432" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCATCAACTCCTTTGGCTTCGGGGGCTCCAACGTGCACATCATCCTGAGGCCCAACACGCAGCCGCCCCCCGCACCCGCCCCACATGCCACCCTGCCCCGTCTGCTGCGGGCCAGCGGACGCACCCC"| __truncated__ "CCCCGCCATCTCATCAATTTATACAGAAATGT" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr9" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "39" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND1->MT-CYB" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3690 14769 .. .. .. .. .. .. .. ..@ width : int [1:2] 311 193 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND1" "MT-CYB" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAAC"| __truncated__ "ACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "20" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "BSG->NFIX" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr19": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 580626 13135835 .. .. .. .. .. .. .. ..@ width : int [1:2] 157 151 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "BSG" "NFIX" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCAACATCCAGCTCCACGGGCCTCCCAGAGTGAAGGCTGTGAAGTCGTCAGAACACATCAACGAGGGGGAGACGGCCATGCTGGTCTGCAAGTCAGAGTCCGTGCCACCTGTCACTGACTGGGCCTG"| __truncated__ "ATGAGTTCCACCCGTTCATCGAGGCACTGCTGCCTCACGTCCGCGCTTTCTCCTACACCTGGTTCAACCTGCAGGCGCGGAAGCGCAAGTACTTCAAGAAGCATGAAAAGCGGATGTCGAAGGACGA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "3" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "KRT7->RP5-857K21.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 52632429 565697 .. .. .. .. .. .. .. ..@ width : int [1:2] 63 191 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "KRT7" "RP5-857K21.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTGAGGGTCCTGAGGAAGTTGATCTCATCATTCAGGGCATCCACCTTGGCCTCCAGCTCCAC" "AACCCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "8" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ATXN7->RP5-947P14.2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr3","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 63898771 106758926 .. .. .. .. .. .. .. ..@ width : int [1:2] 130 159 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ATXN7" "RP5-947P14.2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTGATGCTGGGACAGTCGTGGAATCTGTGGGTTGAGGCTTCCAAACTTCCTGGGAAGGACGGGACAGAATTGGACGAAAGTTTCAAGGAGTTTGGGAAAAACCGCGAAGTCATGGGGCTCTGTCGGG"| __truncated__ "GGTTAAGGTACCAAAAATGCAACATCCTGAAATAAGGAGGTGTTCAAACAATCCAGGTGGCGTCTTCATTACTTGGGGACCAGATGTGCTGTGACAATTGTGCTCAGTGATTGAAGTGACACCCAGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr3" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "30" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "HNRNPA2B1->RP5-857K21.6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr7","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 26235368 566899 .. .. .. .. .. .. .. ..@ width : int [1:2] 149 197 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "HNRNPA2B1" "RP5-857K21.6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACCTCCGTAGCCCCCACCCTGGTTGCCATATCCAGGTCCTCCACCACCATATCCTCCTCTTCCTCCTCCATAACCGGGGCTACCTCCAAAATTGCCACCTCCAGGTCCTCCTCCATACCCATTATAG"| __truncated__ "CCTTACACCTAGCAGGTATCTCCTCTATCTTAGGAGCCATCAATTTCATCACAACAATTATTAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTTTTCGTCTGATCCGTCCTAATCAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr7" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "450" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "HFM1->RN28S1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chrX": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 91852881 108297892 .. .. .. .. .. .. .. ..@ width : int [1:2] 267 181 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "HFM1" "RN28S1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTCGCTATGAACGCTTGGCCGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCCTGCTTAAAACCCAAAAGGTCAGAAGGATCGTGAGGCCCCGCTTTCACGGTCTGTATTCGTACTG"| __truncated__ "AGCGGCTGGTACCCGTTGTTCCTTTCCATGTTTAGCGCTTCCTTCAGGAGCTCTTTTGCGTGCGGCCGGGCGCTTGGCGCCAGAAGCGAGAGCCCCTCAGGGCTCGCCCCCCCGCCTCACCGGGTCA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chrX" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "5" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "SLC38A2->NLRP11" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr19": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 46752715 56299731 .. .. .. .. .. .. .. ..@ width : int [1:2] 175 49 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "SLC38A2" "NLRP11" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GACAGATTCTACGGCACTGCTTTCATTTAATTGGGCTTTAGGCACTCCATTCGAATGCAGAACCTCACCTCTAGTTGAGACCAAGAATTGGCAAATTTGCATGAGCTCCTGGAAAGAGTTGCTGACT"| __truncated__ "TTTTTTTTTTTTTTGTATTGGAAACTGGCAAGAGGGTTTCTCATCATC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2075" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AC092279.1->PRUNE2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr9": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 24184071 79483765 .. .. .. .. .. .. .. ..@ width : int [1:2] 94 37 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AC092279.1" "PRUNE2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CTTCAACTGGAACCCTTCTCCACTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCAAGATCTGCACCTGGGACAGCTCCACC" "CGGGGGGGAAGGAAAGGCTTCTGCCGCTGTACACTA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr9" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "32" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.6->ANKRD30BL" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr2": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 566684 133012886 .. .. .. .. .. .. .. ..@ width : int [1:2] 267 174 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.6" "ANKRD30BL" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GATTATTCCGAAGCCTGGTAGGATGAGAATATAAACTTCAGGGTGACCGAAAAATCAGAATAGGTGTTGGTATAGAATGGGGTCTCCTCCTCCGGCTGGGTCGAAGAAGGTGGTGTTGAGGTTACGG"| __truncated__ "GTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCATATTGCACCGCTAGAGGTGAAATTCTTGGACTGGCAGTTTAGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "4" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "YLPM1->PROX2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr14": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 75287716 75321919 .. .. .. .. .. .. .. ..@ width : int [1:2] 124 108 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "YLPM1" "PROX2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCTAGATATTCGTTCTTTGCTGCAAGATGCTGCTATTGAAGAGGTAGAGATGGAAGATTTTGATGCAAATATCGAAGAACAGAAAGAAGAAAAGAAAGATGCAGAGGAAGAGGAAAGCGAACT" "GGAAGGATCTGAGTCTCTCCCTGCGGAGACAGCCCTGAAGAACTCCTGTAACGTCAAGCTGGCAATTTCCAAGAAGCAATCTGGAACCTGCATTTCCAAAGAGACCC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr14" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "22" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.8->ZNF833P" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr19": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 565613 11777312 .. .. .. .. .. .. .. ..@ width : int [1:2] 189 287 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.8" "ZNF833P" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGTGGGTTTTGTGTGTTCAAACTGTCATTTTATTTTTACGTTGTTAGATATAGGGAGTAGTGTGATTGAGGTGGAGTAGATTAGGCGCAGGTAGAAGTAGAGGTTAAGGAGGGTGATGATGGCTATG"| __truncated__ "AAAAGCCCTGTCAAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTCGGTGGGAATGACAACTTCGGTCGTGGAGGA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "105" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PSMD3->MAFIP" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr21": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 38151371 9826993 .. .. .. .. .. .. .. ..@ width : int [1:2] 156 192 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PSMD3" "MAFIP" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGGCCTCAATGACACCATCCCGGATGGCCTTGGCAACAATGAACTCTGCATCTTCGGGGCTATCCAACTGCAGCTTCTGGGCGATGTCAGCCAAGGAGATTCGGGAATAGGAGAGGCTGATCATGCG"| __truncated__ "GCTCTACCTACCTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr21" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "29" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND1->MT-ND6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3345 14450 .. .. .. .. .. .. .. ..@ width : int [1:2] 140 296 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND1" "MT-ND6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GAATAAATAGGAGGCCTAGGTTGAGGTTGACCAGGGGGTTGGGTATGGGGAGGGGGGTTCATAGTAGAAGAGCGATGGTGAGAGCTAAGGTCGGGGCGGTGATGTAGAGGGTGATGGTAGATGTGGC"| __truncated__ "TTGAGGAGTATCCTGAGGCATGGGGGTCAGGGGTTGAGGTCTTGGTGAGTGTTTTAGTGGGGTTAGCGATGGAGGTAGGATTGGTGCTGTGGGTGAAAGAGTATGATGGGGTGGTGGTTGTGGTAAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "4351" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AC116340.1->AC097532.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr5","chr2": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 71146706 133038453 .. .. .. .. .. .. .. ..@ width : int [1:2] 50 276 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AC116340.1" "AC097532.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AAGAGAACTCTCCCCGGGGCTCCCGCCGGCTTCTCCGGGATCGGTCACG" "TTACCGCACTGGACGCCTCATGGTGCCCATCTCCGCCATTCTGGATTCGGGGATCTGAACCCAACTCCCTTTCAATCAGCTGAGGGCAACAGAGGACATCACCCATCCCTTCGGAATGGCACTCACC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr5" "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "37" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ATP6->MT-CYB" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 8535 14763 .. .. .. .. .. .. .. ..@ width : int [1:2] 52 160 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ATP6" "MT-CYB" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCA" "AAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "C12orf62->LASS5" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 50505971 50558806 .. .. .. .. .. .. .. ..@ width : int [1:2] 111 114 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "C12orf62" "LASS5" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCTGGTTCCGAGTGCTGCGTTCGGCTGTGCTGGGAAGTTGCGTAGACAGTGGCCTCGAGACCCTGCCTGCCTGAGGAGGCCTCGGTTGGATGCGAAGGAGCTGCAGCATC" "CAGAGACTATGGAAGAGAGTACCTGGATCTAGTTTATTCCAAAGACAGACAAGCAGTTTGTGCCTCCACTCCAGGATGACTAACTACAACGATTACACGTAAAAAGACAAAAC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "5" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "FAM107A->DACH1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr3","chr13": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 58551135 72249657 .. .. .. .. .. .. .. ..@ width : int [1:2] 36 121 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "FAM107A" "DACH1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACGATGCAATTCTAGCCAAAAAAAAAAAAAAAAAA" "TTTCTCTTCTTCCTGTTATTGGTAGTTCTGAACGTTAGATATTTTTTTTCCATGGGGTCAAAAGGTACCTAAGTCTATGATTGCGAGTGGAAAAATAGGGGACAGAAATCAGGTATTGGC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr3" "chr13" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "13" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CENPB->RP5-857K21.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr20","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3765611 565772 .. .. .. .. .. .. .. ..@ width : int [1:2] 310 214 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CENPB" "RP5-857K21.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CACCTTCCAGGAAATGCAGAGTAGGGCACTGGGCTTCCTCCTGGGCACCATAAGCCCCGAAGCTGCCACCGGCCTCCACTACTCCCTGGGCCCAGTCCTCAGCCTCCAAGCCCTCCGAGGAGCTCTC"| __truncated__ "AGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCATCATCACCCTCCTTAACCTCTACTTCTAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr20" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "64" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ATP6->MT-ND6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 8676 14449 .. .. .. .. .. .. .. ..@ width : int [1:2] 256 296 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ATP6" "MT-ND6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGGCTTACTAGAAGTGTGAAAACGTAGGCTTGGATTAAGGCGACAGCGATTTCTAGGATAGTCAGTAGAATTAGAATTGTGAAGATGATAAGTGTAGAGGGAAGGTTAATGGTTGATATTGCTAGGG"| __truncated__ "TGAGGAGTATCCTGAGGCATGGGGGTCAGGGGTTGAGGTCTTGGTGAGTGTTTTAGTGGGGTTAGCGATGGAGGTAGGATTGGTGCTGTGGGTGAAAGAGTATGATGGGGTGGTGGTTGTGGTAAAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "289" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RDX->AC140847.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr11","chr12": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 110167088 34372608 .. .. .. .. .. .. .. ..@ width : int [1:2] 175 88 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RDX" "AC140847.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGCGCTCAGTCCGCGGCGCGAGGACGGCCGGCCGGCAGGGGGAGGCGGGGGGGCGCCGGGCAGCCCCGCCTTTTCCCGCGGAGGCGCCGAGCGGCCATATTGCGGAGCTGTCTGCGGTGGCGGCGGC"| __truncated__ "AGCCAAGCACATACACAAAATGTCTGAACCTGCGGTTCCTCTCGTACTGAGCAGGATTACCATGGTAGCAACACATGGGCAACAACA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr11" "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "11" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CTB-161M19.3->NPM1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr5": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 118309491 170814948 .. .. .. .. .. .. .. ..@ width : int [1:2] 81 45 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CTB-161M19.3" "NPM1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CATCTACCTCATTGTCAGCCTCCTGCTCCCCATTTTCCTCATTAGCATTCCCGTTAGCAGGGGCGTCTCTTCCATTTTCT" "ACCCGATGGAAGATTCGATGGACATGGACATGAGCCCCCTGAGG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "197" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND4->MT-ND2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 11870 5263 .. .. .. .. .. .. .. ..@ width : int [1:2] 235 230 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND4" "MT-ND2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCAC"| __truncated__ "CCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCAT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "27" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PCBP2->PCBP2P3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 53858379 91139848 .. .. .. .. .. .. .. ..@ width : int [1:2] 247 61 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PCBP2" "PCBP2P3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCAACTCAACTGAGCGGGCCATCACTATTGCTGGCATTCCACAATCCATCATTGAGTGTGTCAAACAGATCTGCGTGGTCATGTTGGAGTCCCCCCCGAAGGGCGTGACCATCCCGTACCGGCCCAA"| __truncated__ "CACCTCTAGAGTTGACCAAGCTGCACCAGTAGGCAATGCAACAGGCTTATTTTCCCATGA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "427" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND4->MT-ND1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 11866 3340 .. .. .. .. .. .. .. ..@ width : int [1:2] 238 233 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND4" "MT-ND1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTA"| __truncated__ "CCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "8" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP11-488L18.4->RP11-488L18.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr1": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 247365296 247373994 .. .. .. .. .. .. .. ..@ width : int [1:2] 103 149 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP11-488L18.4" "RP11-488L18.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCTGAACCCAGACACATTCACCTGAGAACCAGCCATTTCTTCCTCTTCTTCCTTCTTCTCTGGGATTCCTTCTCAGGTGAGATTATCTGGACAAATCACACC" "ATTTCCCAGCTTCCCGGGTGTCCAGGCTGCTTAGCTATGGATCTCCTGATACCTGCAGGTCAGAGGGCAAGAGGCTGTGGCGGCCACCTGAGCTTCCCCGAGCAAAGCACGCCGAGCACAGAAGACG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "28" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "GAPDH->RP5-857K21.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 6646564 569305 .. .. .. .. .. .. .. ..@ width : int [1:2] 316 189 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "GAPDH" "RP5-857K21.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGGGAGCCAAAAGGGTCATCATCTCTGCCCCCTCTGCTGATGCCCCCATGTTCGTCATGGGTGTGAACCATGAGAAGTATGACAACAGCCTCAAGATCATCAGCAATGCCTCCTGCACCACCAACTG"| __truncated__ "TTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCGCTC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "16" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.4->H19" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr11": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 568816 2019070 .. .. .. .. .. .. .. ..@ width : int [1:2] 216 249 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.4" "H19" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ATTTGTTTTGAGGTTAGTTGGATTAGTCATTGTTGGGTGGTAATTAGTCGGTTGTTGATGAGATATTTGGAGGTGGGGATCAATAGAGGGGGAAATAGAATGATCAGTACTGCGGCGGGTAGGCCTA"| __truncated__ "GGTGAGGGAGGGGGTGGGATGGGTGGGGGGTAACGGGGGAAACTGGGGAAGTGGGGAACCGAGGGGCAACCAGGGGAAGATGGGGTGCTGGAGGAGAGCTTGTGGGAGCCAAGGAGCACCTTGGACA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr11" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "23" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PMS2->RP11-313P13.3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr7": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 6045509 72476697 .. .. .. .. .. .. .. ..@ width : int [1:2] 149 156 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PMS2" "RP11-313P13.3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTAAGCTTTAGATCAATATTAGTGGCACCAGCATCCAGACTGTTTTCTACTAACTCCTTTACCGCAGTGCTTAGACTCAGTACCACCTGCCCAGAGCAAATCTGATGGACTGACTTCCGATCAATAG"| __truncated__ "CTCGAGCTCTCAGCTCTCTCCAAGGATGCAACACCGGATCCGCCTCGGGGACTGGGAAAGTGCCCTCAACGGCTCCCACAGGCGCCCCGCCTCCTGGGCTCCCATTGGCTGCTTTCGACGTTGTGCT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr7" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ANAPC1->AC093616.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr2": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 112560911 88038531 .. .. .. .. .. .. .. ..@ width : int [1:2] 120 157 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ANAPC1" "AC093616.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGCATAGGGAGAAACATAAATCACCAAGTTATCAAATCAAAGAAGGAGATACCATAAATGTGGATGTGACTTGTCCAGGTGCTACTCTAGCTTTGGCTATGATCTACTTAAAAACCAAT" "AACAGTGTCTTCTAGGAAGCCCAGACACATGGAGAAGTTCTGAGTGTTTTGGCCGATAGTCCCAGATGAGGTTCCAGCAACAGCTGGGATCACCCATGAGATGTGAGTGAGGAAGGCTTTGAGATGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "GAPDH->EEF2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr19": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 6646774 3984152 .. .. .. .. .. .. .. ..@ width : int [1:2] 193 323 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "GAPDH" "EEF2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTGCGGCTCCCTAGGCCCCTCCCCTCTTCAAGGGGTCTACATGGCAACTGTGAGGAGGGGAGATTCAGTGTGGTGGGGGACTGAGTGTGGCAGGGACTCCCCAGTGTAGCCCAGGATGCCCTTGAGG"| __truncated__ "GCATCACCATCAAGTCAACTGCCATCTCCCTCTTCTACGAGCTCTCGGAGAATGACTTGAACTTCATCAAGCAGAGCAAGGACGGTGCCGGCTTCCTCATCAACCTCATTGACTCCCCCGGGCATGT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP11-343L14.2->PCBD2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 115078884 134263386 .. .. .. .. .. .. .. ..@ width : int [1:2] 201 160 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP11-343L14.2" "PCBD2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCTGACACAGCAGGCAAGTCCACAGCAGCCCCAGGAAGGTTCACACCCTTCTTGCTGCCCGAGGAACCACCAGTTTCCACCTCCGTCACCAGGAAGTCAGCACCTTTCTGCTTTACCTGGAGAGAAA"| __truncated__ "AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCCTGGCTATCATCACCCGATGAGGCAACCAACCAGAACGCCTGAACGCAGGTACATACTTCCTATTCTACACCCTAGTAGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "11" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "NCL->RP5-857K21.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 232325321 565854 .. .. .. .. .. .. .. ..@ width : int [1:2] 93 167 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "NCL" "RP5-857K21.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCTGCTTTCTGTTTGGCCATTTCCTTCTTTCGTTTTCCAGGTGCTTCTTTGACAGGCTCTTCCTCCTCCTCTTCTTCCTCCTCCTCATCATC" "CCCACCATCATAGCCATCATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATATCTAACAACGTAAAAATAAAATGACAGTTTGAACACACAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PTMA->SET" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr9": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 232577002 131456256 .. .. .. .. .. .. .. ..@ width : int [1:2] 169 113 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PTMA" "SET" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AAGTTGTGGAAGAGGCAGAAAATGGAAGAGACGCCCCTGCTAACGGGAATGCTGAGAATGAGGAAAATGGGGAGCAGGAGGCTGACAATGAGGTAGACGAAGAAGAGGAAGAAGGTGGGGAGGAAGA"| __truncated__ "GACGAAGAAGGGGATGAGGATGAAGGTGAAGAAGATGAAGATGATGATGAAGGGGAGGAAGGAGAGGAGGATGAAGGAGAAGATGACTAAATAGAACACTGATGGATTCCAA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr9" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "4" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "STYXL1->TMEM120A" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr7": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 75625599 75621876 .. .. .. .. .. .. .. ..@ width : int [1:2] 166 92 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "STYXL1" "TMEM120A" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCACTTCATTGAGGTCCTGGGCCTATGTCAAGAAGTGCAAAAACAACATGTGTCCAAATCGGGGATTGGTGAGCCAGCTGCTGGAATGGGAGAAGACTATCCTTGGAGATTCCATCACAAACATCAT"| __truncated__ "GGAGACCCATCGGCTCTACCGCCTGAAGCTGGAGGAGCTGACCAAACTTTAGAACAATTGCACCAGCTCCATCACGCGGCAGAAGAAGCGG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr7" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "11" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "SET->CTB-161M19.3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr9","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 131456149 118309652 .. .. .. .. .. .. .. ..@ width : int [1:2] 95 161 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "SET" "CTB-161M19.3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCCAAACCCATTACAGTACTACTTGGTTCCCGATATGGATGATGAAGAAGGAGAAGGAGAAGAAGATGATGATGATGATGAAGAGGAGGAAGGA" "AGAAGAGGAAGAAGGTGGGGAGGAAGAGGAGGAGGAAGAAGGTGATGGTGAGGAAGAGGATGGAGATGAAGATGAGGAAGCTGAGACAGCTACGGGCAAGCGGGCAGCTGAAGATGATGAGGATGAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr9" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "UBA52->CAPN2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 18682493 223964599 .. .. .. .. .. .. .. ..@ width : int [1:2] 205 151 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "UBA52" "CAPN2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGACTCTTTCTGGATGTTGTAGTCTGAGAGAGTGCGGCCATCCTCCAGCTGTTTGCCGGCAAATATCAGACGCTGCTGGTCAGGTGGGATACCCTCCTTGTCTTGAATTTTGGCTTTGACATTCTCA"| __truncated__ "TGCTAATGCCTGTTTTACAGCGGGCAAAAATAGATAGATACGCAAATAGATGATAAGCAAAGTAAAGCTCAACTTTCTGAGCCTGTACGAACTCACCACCCCCCGCCCCCCCGCCGCCACCAACCCT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "17" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.4->RP11-642N14.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr3": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 568875 75264418 .. .. .. .. .. .. .. ..@ width : int [1:2] 141 183 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.4" "RP11-642N14.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GAAATAGAATGATCAGTACTGCGGCGGGTAGGCCTAGGATTGTGGGGGCAATGAATGAAGTGAACAGATTTTCGTTCATTTTGGTTCTCAGGGTTTGTTATAGTTTTTTATTTTTATGGGCTTTGGT"| __truncated__ "GGTAGTTATGGAGGAGGTGATGGTGGATATAATGGATTTGGAGGTGATGGTGGCAACTATGGCGGTGGTCCTGGTTATAGTAGTAGAGGGGGCTATGGTGATGGTGGACCAGGATATGGAAACCAAG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr3" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "27" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "IKZF3->VAPB" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr20": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 37933808 56964573 .. .. .. .. .. .. .. ..@ width : int [1:2] 213 231 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "IKZF3" "VAPB" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGCTTGGTCCATCATGCGGGTCTGTATGAGCTCACTCTCTTTCTCATACATGTAACTTGAATTATAGTTGACATCAAAGCAGTGGCGCTTCTCACCAATGAATTTCTGAGGCATTGAGCTTTTTCGT"| __truncated__ "CTCGGAATTTGAGCTCGTGCTGCGGCTCGAGGCTCAGGACCTGCTCCACCTTCGCCATGTTCCTTAGCGGCGGAGCACCTTTGGCGGGGAGACCCCTGAGAGGTCACCGGGGCGGGAAGCGTTAATG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr20" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "HNRNPUL1->HIVEP1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr6": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 41811395 12011227 .. .. .. .. .. .. .. ..@ width : int [1:2] 228 332 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "HNRNPUL1" "HIVEP1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGCAACAGCCGCCACCACAGCAGCCTCCGCCACCACAGCCACCACCCCAGCAGCCACCGCCACCACCCAGCTACAGCCCTGCTCGGAACCCCCCAGGGGCCAGCACCTACAATAAGAACAGCAACAT"| __truncated__ "CAGGGGTTAATTGCGCTCGCAGCTTCGGCACTGGGAAGCACCAGCGGGGCTTTGGAGCGGCCTCTGGAATAACCTTGGCTTTCCTCGCTCTTTTAATAGAACATCCGCCACCAAAAAGTGGTTTCAG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr6" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "3" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "GCN1L1->MSI1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 120627980 120785317 .. .. .. .. .. .. .. ..@ width : int [1:2] 122 154 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "GCN1L1" "MSI1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ATGGCGGCGGACACGCAGGTTTCCGAGACACTAAAGCGTTTTGCAGGGAAGGTGACAACAGCCAGTGTAAAGGAACGGAGAGAAATCCTCAGTGAACTTGGGAAGTGTGTTGCTGGAAAAG" "CCATTCCTCTCACTGCCTACGGACCAATGGCGGCGGCAGCGGCGGCAGCGGCTGTGGTTCGAGGGACAGGCTCTCACCCCTGGACGATGGCTCCCCCTCCAGGTTCGACTCCCAGCCGCACAGGGGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "85" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "BOLA2B->SMG1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr16": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 30204578 18891041 .. .. .. .. .. .. .. ..@ width : int [1:2] 102 275 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "BOLA2B" "SMG1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGGAGGTGGAGGACACGACCCTCAACCGTTGCTCCTGTAGCTTCCGAGTCCTGGTGGTGTCGGCCAAGTTCGAGGGGAAACCGCTGCTTCAGAGACACAGG" "TTCTGTACAGAGTAATGAGATGTGTGACGGCTGCAAACCAGGTGTTTTTTTCTGAGGCTGTGTTGACAGCTGCTAATGAGTGTGTTGGTGTTTTGCTCGGCAGCTTGGATCCTAGCATGACTATACA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr16" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "18" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RPL13A->RP5-857K21.6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 49994855 567753 .. .. .. .. .. .. .. ..@ width : int [1:2] 145 96 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RPL13A" "RP5-857K21.6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCCGTACATTCCAGGGCAACAATGGAGGAAGGGCAGGCAACGCATGAGGAATTAACAGTCTTTATTGGGCTCAGACCAGGAGTCCGTGGGTCTTGAGGACCTCTGTGTATTTGTCAATTTTCTTCTC"| __truncated__ "ATCCGGAATGCCCCGACGTTACTCGGACTATCCCGATGCATACACCACATGAAATATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "51" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ATP6->MT-ND6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 8352 14333 .. .. .. .. .. .. .. ..@ width : int [1:2] 216 180 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ATP6" "MT-ND6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GAGGAGGTTAGTTGTGGCAATAAAAATGATTAAGGATACTAGTATAAGAGATCAGGTTCGTCCTTTAGTGTTGTGTATGGTTATCATTTGTTTTGAGGTTAGTTTGATTAGTCATTGTTGGGTGGTG"| __truncated__ "TTGTGGTAAACTTTAATAGTGTAGGAAGCTGAATAATTTATGAAGGAGAGGGGTCAGGGTTGATTCGGGAGGATCCTATTGGTGCGGGGGCTTTGTATGATTATGGGCGTTGATTAGTAGTAGTTAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "4" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PPP1R3F->RP5-968D22.3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chrX","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 49157615 168454952 .. .. .. .. .. .. .. ..@ width : int [1:2] 288 78 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PPP1R3F" "RP5-968D22.3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACAGCCCGAGTGCCAGGGTCCCGTGGAGGCTGAGGCCAGGCAGCTGAAGAGCTGCATGAAGCCGGTGAGGCGCAGGCCTGCCGAGGAGGAACTGAAGACGAAGAACATGGATGATAACACCTTTGCC"| __truncated__ "GGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATCACCGGCAGAGGCTGCAGAGCAGCAAAGATTGCTGCCTGCTCC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chrX" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "C10orf140->SCD" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr10": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 21811150 102123485 .. .. .. .. .. .. .. ..@ width : int [1:2] 51 135 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "C10orf140" "SCD" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACAAACGTATATGGTGAAGAGCTGGTGGCGGGGGGGGGGGGGGGGGGGGG" "GTCTGCTGAGTAAGGAACACGATTTTCAAGATTCTAAAGCTCAATTCAAGTGACACATTAATGATAAACTCAGATCTGATCAAGAGTCCGGATTTCTAACAGTCCTTGCTTTGGGGGGTGTGCTGAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr10" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "14" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "EEF2->RP5-857K21.6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3981768 566882 .. .. .. .. .. .. .. ..@ width : int [1:2] 178 260 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "EEF2" "RP5-857K21.6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGGTGGATGGTGATCATCTGCAACAAGGCGTCTCCGGCAGGCAGCCAGCGGCGCATCACAGCCTTCAGCAGGGGTTTGCCTTCTTTGTCCTTGTCCTCGCTGTCCAGTTTGATGTCCAGTTTCTCTA"| __truncated__ "AGACCTAACCATCTTCTCCTTACACCTAGCAGGTATCTCCTCTATCTTAGGAGCCATCAATTTCATCACAACAATTATTAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTTTTCGTC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "23" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "APP->RP5-857K21.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr21","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 27423161 565832 .. .. .. .. .. .. .. ..@ width : int [1:2] 233 184 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "APP" "RP5-857K21.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AATGCTGGTGGTTCTCTCTGTGGCTTCTTCGTAGGGTTCCTCAGCCTCTTCCTCTACCTCATCACCATCCTCATCGTCCTCGTCATCATCGGCTTCTTCTTCTTCCACCTCAGCCACTTCTTCCTCC"| __truncated__ "AAAAAACAATAGCCTCATCATCCCCACCATCATAGCCATCATCACCCTCCTTAACCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATATCTAACAACGTAAAAATA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr21" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "94" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ACTB->CCDC73" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr7","chr11": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 5567042 32767349 .. .. .. .. .. .. .. ..@ width : int [1:2] 250 94 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ACTB" "CCDC73" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGGACTGGGCCATTCTCCTTAGAGAGAAGTGGGGTGGCTTTTAGGATGGCAAGGGACTTCCTGTAACAACGCATCTCATATTTGGAATGACTATTAAAAAAACAACAATGTGCAATCAAAGTCCTCG"| __truncated__ "AAATAAAGGGATGGAGGAGGATATACCAAGCAAATGGAAAGCAAAAAAAAAAAAAAAACCAAAACAAACAAACAAACAAAAAAACAAAAACCA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr7" "chr11" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "30" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.4->ATP5G3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr2": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 569580 176043940 .. .. .. .. .. .. .. ..@ width : int [1:2] 187 112 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.4" "ATP5G3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGCCTAGTATGAGGAGGGTTGTGGAGTGGAAGTGAAATCACATGGCTAGGCCGGAGGTCATTAGGAGGGC"| __truncated__ "TCAGCTAATCCAAAGGGAGTTTCAGACCAGTGCAATCAGCAGAGACATTGATACTGCTGCCAAATTTATTGGTGCAGGTGCTGCAACAGTAGGAGTGGCTGGTTCTGGTGC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "10" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "VAMP8->VAMP5" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr2": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 85808903 85811616 .. .. .. .. .. .. .. ..@ width : int [1:2] 96 175 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "VAMP8" "VAMP5" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GAGGGTCTCCTTTCCTGTCTTCCTCTACAGAGAATGCTGCTCGGTCCTCCTACCCCTCTTCCCGAGGCCCTGCTGCCATGTTGTATGCCCCAGAA" "GGCAGGAATAGAGTTGGAGCGGTGCCAGCAGCAGGCGAACGAGGTGACGGAAATTATGCGTAACAACTTCGGCAAGGTCCTGGAGCGTGGTGTGAAGCTGGCCGAACTGCAGCAGCGTTCAGACCAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "1" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP11-959I15.3->PARP1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr8","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 125184221 226595697 .. .. .. .. .. .. .. ..@ width : int [1:2] 38 115 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP11-959I15.3" "PARP1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AAGGATTGAGGCCCTGAGTTTGGGCGGCGGGGGGGGG" "CGAGGCGGCAGCGTGTTTCTAGGTCGTGGCGTCGGGCTTCCGGAGCTTTGGCGGCAGCTAGGGGAGGATGGCGGAGTCTTCGGATAAGCTCTATCGAGTCGAGTACGCCAAGAG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr8" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2629" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AC092279.1->KRT19" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr17": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 24184067 39684563 .. .. .. .. .. .. .. ..@ width : int [1:2] 87 204 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AC092279.1" "KRT19" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCATCTTCAACTGGAACCCTTCTCCACTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCAAGATCTGCACCTGGG" "GCCGCTCCTCCCGCGAATCGCAGCTTCTGAGACCAGGGTTGCTCCGTCCGTGCTCCGCCTCGCCATGACTTCCTACAGCTATCGCCAGTCGTCGGCCACGTCGTCCTTCGGAGGCCTGGGCGGCGGC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr17" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "24" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CDK12->U6.891" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr17": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 37687094 37700501 .. .. .. .. .. .. .. ..@ width : int [1:2] 180 111 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CDK12" "U6.891" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCCAAACAGGACTTATGGAAACACTGATGGGCCTGAAACAGGGTTCAGTGCCATTGACACTGATGAACGAAACTCTGGTCCAGCCTTGACAGAATCCTTGGTCCAGACCCTGGTGAAGAACAGGACC"| __truncated__ "GGTAGGAGCAACGGTGGGAATGCCCTCTGAGGAATGCAGTGATGTCCATCAGTCACCTCTCACCCAGAGCCTGGCAAATTCAGTCTCTTTCACAGAACCTAAAGCCAAGC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr17" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "38" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RPL23->RP5-857K21.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 37009529 568792 .. .. .. .. .. .. .. ..@ width : int [1:2] 267 323 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RPL23" "RP5-857K21.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTTTTTCTGAGCTCTGGTTTGCCTTTCTTGACTGTGGCCATCACCATGTCACCCACACCAGCAGCGGGAAGTCTGTTCAGCCGTCCCTTGATCCCCTTCACGGAGATGATATACAGGTTTTTGGCTC"| __truncated__ "GAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "230" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-CO2->MT-ND4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 7596 10867 .. .. .. .. .. .. .. ..@ width : int [1:2] 272 276 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-CO2" "MT-ND4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTC"| __truncated__ "CATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "37" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "J01415.2->MT-CO1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 250 6334 .. .. .. .. .. .. .. ..@ width : int [1:2] 130 269 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "J01415.2" "MT-CO1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACAC"| __truncated__ "ACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "16" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PTMA->RP5-857K21.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 232577022 568365 .. .. .. .. .. .. .. ..@ width : int [1:2] 155 175 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PTMA" "RP5-857K21.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TGAATAGGTCACGGCGGCCTTTTTTTTTTTAGTTTAACTTTTCCTTTTTTGCTGTCTAGTCATCCTCGTCGGTCTTCTGCTTCTTGGTATCGACATCGTCATCCTCATCATCTTCAGCTGCCCGCTT"| __truncated__ "GCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCTTTACCATCAAATCAATTGGCCATCAATGGTACTGAACCTACGAATACACCGACTACGGCGGACTAATCTTCA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "148" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.9->HFM1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr1": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 564211 91853147 .. .. .. .. .. .. .. ..@ width : int [1:2] 242 115 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.9" "HFM1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTCAGAAGTAGGGTCTTGGTGACAAAATATGTTGTGTAGAGTTCAGGGGAGAGTGCGTTATATGTTGTTCCTAGGAAGATTGTAGTGGTGA"| __truncated__ "CCGGGGACAGTGCCAGGTGGGGAGTTTGACTGGGGCTGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGG" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "7" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "TUBA1B->CTB-36O1.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr12","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 49521658 134263898 .. .. .. .. .. .. .. ..@ width : int [1:2] 274 259 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "TUBA1B" "CTB-36O1.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGAAAGCTTTAACGTCTGTCAGTTAAGCTGAAGCTGAAATTCTGGGAGCATGACATGCTGCAGGGCCAAAAGGAATGGATAATTAGTATTCCTCTCCTTCTTCCTCACCCTCTCCTTCAACAGAATC"| __truncated__ "TATTCATTATAGCCACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTACCTATCGCCATACTAGTCTTTGCTGCCTGCAAGGCAGCAGTAGGCCTAGCCCTACTAGTCTCAATCTC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr12" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "175" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PIGU->RN28S1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr20","chrX": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 33169170 108297603 .. .. .. .. .. .. .. ..@ width : int [1:2] 217 177 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PIGU" "RN28S1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CGCAGGAAGGCATAGAAGTAATCAGAGATGAGCAGGATCTGCCCAACGTTGAAGGTCAGTGTGATGGCATAAAAGAAATTAGAGTTGGCACTTCCTGCATAAATCCAGAGGTGCCACAGGACAGGGA"| __truncated__ "CTGTTGAGCTTGACTCTAGTCTGGCACGGTGAAGAGACGTGAGAGGTGTAGAATAAGTGGGAGGCCCCCGGCGCCCCCCGGTGTCCCCGCGAGGGGTCCAGGGCGGGGTCTGCCGGCCCTGCGGGCC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr20" "chrX" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "27" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "SBNO1->RP13-942N8.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 123834778 123849248 .. .. .. .. .. .. .. ..@ width : int [1:2] 211 156 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "SBNO1" "RP13-942N8.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TACAGTCTCTGGTTCTTGTTTAACAGGAACTGCTGCTTCGGTCTCCAAACCTAGTTCTAATGCACTAAGTGGCACTGACTGCTGAACTGACGGGGTAGGCATTGGAGTTGCAAGCCCTGCATCTCCA"| __truncated__ "TTTCCCCGCGGGACCCGGCGCCAGCACAGCTCCTCCCGGGAGGTGTGAGTTTGAAGGACCAGAGGCGACTGGAGCGGAGGCGGCGGTGGCGGCGGCAGCAGCGGCGTCCTGCTCTGCCTACCTCCCC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "350" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP5-857K21.9->AC097532.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr2": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 564236 133038727 .. .. .. .. .. .. .. ..@ width : int [1:2] 249 91 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP5-857K21.9" "AC097532.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTCAGAAGTAGGGTCTTGGTGACAAAATATGTTGTGTAGAGTTCAGGGGAGA"| __truncated__ "GCCACAGGTGCAGATCTTGGTGGTAGTAGCAAATTTTCAAATGAGAACTTTGAAGGCCGAAGTGGAGAAGGGTTCCATGTGAACAGCAGT" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "8" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "GSTM2->NUDT19" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr1","chr19": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 110212251 33185000 .. .. .. .. .. .. .. ..@ width : int [1:2] 84 98 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "GSTM2" "NUDT19" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GAAGGAAGAAACTGCGGACACATCTGAACATCTGAAGGAACAAACTCCGGACACACCATCTTTAAGAACTGTAACACTCACCG" "AATCAAGGCCATCAAACTACAGATGGTCTTACAAACGGAAACCCAAATGAGCTCAACTAACAACTTCTACCGAGGACCCCTGGACCGACCCACTGGC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr1" "chr19" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "3" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ACTB->HNRNPD" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr7","chr4": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 5570138 83294802 .. .. .. .. .. .. .. ..@ width : int [1:2] 39 169 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ACTB" "HNRNPD" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CATCATCCATGGTGAGCTGGCGGCGGGTGTGGACGGGC" "GGCGGCGGCAGCGGCAACGGCGGCGGTAGGCGGCTCGGCGGGCGAGCAGGAGGGAGCCATGGTGGCGGCGACACAGGGGGCAGCGGCGGCGGCGGGAAGCGGAGCCGGGACCGGGGGCGGAACCGCG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr7" "chr4" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "16" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "PTMA->RP5-857K21.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 232575906 568953 .. .. .. .. .. .. .. ..@ width : int [1:2] 189 270 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "PTMA" "RP5-857K21.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCCCGCTTGCCCGTAGCTGACTCAGCTTCCTCATCTTCATCTCCATCCTCTTCCTCACCATCACCTTCTTCTTCCTCCTCCTCTTCCTCCCCACCTTCTTCCTCTTCTTCGTCTACCTCATTGTCAG"| __truncated__ "TACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAATACAAATTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAACTATAACAAACCCTGAGAACCAAAATGA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "5" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "TAOK1->FTH1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr11": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 27717234 61734972 .. .. .. .. .. .. .. ..@ width : int [1:2] 332 119 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "TAOK1" "FTH1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCCAGCCCAAGCTCTGCAACAAGGGGCGGCGGCGGCGGGGGGTGGGGGGGGGGGCGAGGGGACGACCGGGGTCGAGGAGGCGCCCTCAGCGCTTGGGCTCAGTTAAGATGGCGCGGGGAAGTGCCGG"| __truncated__ "AGTCCGAGGGTGCGGTGAAGAGGTGACGGAGGGCTGGCTATGGGCGGCCGGCCGGGGTGGGGAACGAGCGCCGGGTTCCGTCCAAGCACTGTTGAAGCAGGAAACCCCGACGACTCTC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr11" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "7" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CALR->RP5-857K21.8" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 13054361 565886 .. .. .. .. .. .. .. ..@ width : int [1:2] 213 117 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CALR" "RP5-857K21.8" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGCCAGCTCTGCGGCAGGAGCGCTCAGGCCTCAGTCCAGCCCTGGAGGCAGGCCTCTCTACAGCTCGTCCTTGGCCTGGCCGGGGACATCTTCCTCCTCATCTTCCTCCTTGTCCTCCTCATCCTCC"| __truncated__ "CCTCTACTTCTACCTGCGCCTAATCTACTCCACCTCAATCACACTACTCCCTATATCTAACAACGTAAAAATAAAATGACAGTTTGAACACACAAAACCCACCCCATTCCTCCCCA" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "195" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "BCAS3->BCAS4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr17","chr20": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 59445527 49411710 .. .. .. .. .. .. .. ..@ width : int [1:2] 162 146 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "BCAS3" "BCAS4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCCGGATCCCACGACGTCCCGGCTAGGTGACTCGGCCATGGCGTCGGCAAGTCGCTCCCGGAGGCCCTCCTCCGTGTGCTCCATGGAGGACATGTGCCGCAGCCCGAAGCCCTCAGGCCAGCTCCCG"| __truncated__ "TACCTCGGCCCCAGGCTCGGGGGTCAGGAAGAGCGCGAGCTCGCGCGCCCCGCTGCGCATGGGCTCCGGCTGATCAGCGTCCACGAGCAGCATCAGGAGGGCGACGGGGTCCGGCTGGCGGAGGCTG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr17" "chr20" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "26" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CTB-161M19.3->PCBD2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr5": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 118309533 134263619 .. .. .. .. .. .. .. ..@ width : int [1:2] 71 328 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CTB-161M19.3" "PCBD2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCCCCACCTTCTTCCTCTTCTTCATCTACCTCATTGTCAGCCTCCTGCTCCCCATTTTCCTCATTAGCAT" "CATCCCCCTACTATTTTTCAACCAAATCAACAACAACCTATTTAGCTGCTCCTTATCCTTCTCCTCCGACCCCCTAACGACCCCCCTCCTAATACTAACTACCTGACTCCTGCCCCTCACAATCATG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "7" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RP11-20F24.2->RP11-20F24.3" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr10": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 37531684 37537043 .. .. .. .. .. .. .. ..@ width : int [1:2] 89 138 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RP11-20F24.2" "RP11-20F24.3" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGTAAACAAATTGCTCCTGTGGAGATGATTGGCATCACATGGTGTTTTGAGCTGATACACCCAACACTTGAGCTCACTGCAACAGTAC" "CAGATTTTCACCGCTATGCCTCCTTTCACTCTGGGAGTCTTCCAGAGGTCTTGCACTCGGGAGAGCATGCTCAGGTTTCCCCAGCTCTACAAAATCACCCAGAATGCCAAAGACTTCAACACAAGGG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr10" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "9" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "H19->CTB-36O1.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr11","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 2018819 134263935 .. .. .. .. .. .. .. ..@ width : int [1:2] 211 77 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "H19" "CTB-36O1.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCTGATGTCGCCCTGTCTGCACGATGCCTGGGCGCCTACTCCACACTCCTCACTGGCCTCAGGCCCCACCAGCCCTGCCTCGAGCTAGCCCCTCCACCCGTCATCACTCCTGCCAGACTCCAGATGT"| __truncated__ "TCCTCCCTACTATGCCTAGAAGGAATAATACTATCACTATTCATTATAGCCACTCTCATAACCCTCAACACCCACT" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr11" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "65" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CTD-2165H16.1->PCBD2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr5": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 14652368 134263010 .. .. .. .. .. .. .. ..@ width : int [1:2] 166 169 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CTD-2165H16.1" "PCBD2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCAGCGCTTATTTGGCCTGGATGGTTCAGGATAATCACCTGAGCAGTGAAGCCAGCTGCTTCCATTGGTGGGTCATTTTTGCTGTCACCAGCAACGTTGCCACGACGAACATCCTTGACAGACACAT"| __truncated__ "CGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACATATAGCCTACCCCTTCCTTGTACTATCCCTGTGAGGCATAATTATAACAAGCTCCATCTGCCTGCGACAAACAGAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "8" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RPL7A->RP5-857K21.6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr9","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 136216740 567008 .. .. .. .. .. .. .. ..@ width : int [1:2] 141 234 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RPL7A" "RP5-857K21.6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTACGACACAGGGCAGGCAAGAAGACAACCAGCTCGATGGGATCCACGTCGTGTGCAATCACCACCAGCTGAGCTTTCTTGTTCTCCACCAAGGTGGTGACGGTGTTAACTCCTGCTCGAAGGACAG"| __truncated__ "CTGATCCGTCCTAATCACAGCAGTCTTACTTCTCCTATCTCTCCCAGTCCTAGCCGCTGGCATCACTATACTACTAACAGACCGTAACCTCAACACCACCTTCTTCGACCCAGCCGGAGGAGGAGAC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr9" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "5" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ATRN->RPS14" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr20","chr5": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3596349 149822838 .. .. .. .. .. .. .. ..@ width : int [1:2] 240 83 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ATRN" "RPS14" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TTTCAAAAACCAACATTAAGGAGTACAAAGATAGTTTCTCTAATGAGAAGTTTGATTTTCGCAACCACCCAAATATCACTTTCTTTGTTTATGTCAGTAATTTCACCTGGCCCATCAAAATTCAGGT"| __truncated__ "TAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTATACATATGTAACAAACCTGCACGTTGTGCACATGTAC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr20" "chr5" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "29770" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MAFIP->UNC45B" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr21","chr17": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 9827020 33478116 .. .. .. .. .. .. .. ..@ width : int [1:2] 184 146 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MAFIP" "UNC45B" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACT"| __truncated__ "CGTACGCCACATTTCCCGCGCCCCACCGCGGGGCGGGGATTCGGCGCTGGGCTCTTCCCTGTTCACTCGCCATTACTGAGGGAATCCTGGTTAGTTTCTTTTCCTCCGCTGACAAATATGCTTAAAT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr21" "chr17" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "10" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND5->MT-ND4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 13848 10820 .. .. .. .. .. .. .. ..@ width : int [1:2] 323 122 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND5" "MT-ND4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAA"| __truncated__ "CACATAATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "10" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ATP6->MT-ND5" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 9018 12740 .. .. .. .. .. .. .. ..@ width : int [1:2] 179 319 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ATP6" "MT-ND5" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "ACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCG"| __truncated__ "ACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTAT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "81" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "RGPD2->HFM1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 88124571 91853055 .. .. .. .. .. .. .. ..@ width : int [1:2] 99 269 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "RGPD2" "HFM1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GTCATTGTTGGGTGGTAATTAGTCGGTTGTTGATGAGGTATTTGGAGGTGGGGATCAATAGAGGGGGAAATAGAATGATCAGTACTGCGGCGGGCAGA" "AACCTCCCGTGGAGCAGAAGGGCAAAAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGGGGCCTCACGATCCTTCTGACCTTTTGGGTTTTAAGCAGGAGGTGTCAGAAAAG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "789" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "AC092279.1->AC097532.1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr19","chr2": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 24183988 133038650 .. .. .. .. .. .. .. ..@ width : int [1:2] 92 42 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "AC092279.1" "AC097532.1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCCTGGGTGGAGCTGTCCCAGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGTGGAGAAGGGTTCCA" "TGTGAACAGCAGTTGAACATGGGTCCCAGGTGAACAGCAGT" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr19" "chr2" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "1" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "CDCA4->APBB2" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr14","chr4": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 105487148 41218468 .. .. .. .. .. .. .. ..@ width : int [1:2] 200 64 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "CDCA4" "APBB2" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGACTGAGCGGCACAGGTTGGGCTCCACAAGCATGTGGCAAAGCTGCAACTTCACCAGAGACATGTCCAGGAGCGACTGCCGCTGCAGGCTGTATGAGGACACTGTCTTCAAGCCGGCCAGGGCTCC"| __truncated__ "GCCGCCCCGCCCCCCCCCCCCCCCCCCCCCCCGCCGCCGCGGACTCCACCGCGGGTTTTCCTC" .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr14" "chr4" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "176" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "TMSB10->SLCO5A1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr2","chr8": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 85132441 70602288 .. .. .. .. .. .. .. ..@ width : int [1:2] 326 229 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "TMSB10" "SLCO5A1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "AGTGCAGCTTGTGGCTCGTGTCCATCTTGCAGGTGGCTCTTCCTCCACATCACGACTGGGGTCTCGAAGAGGACGGGGGTAGGAAATCCTCCAGGATCTTAGGAAATTTCACTCCGCTTCTCCTGCT"| __truncated__ "GGGGGGGCGCCAGGGGCCTCCCACTTATTCTACACCTCTCATGTCTCTTCACCATGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTG"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr2" "chr8" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "SMARCD3->FTH1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr7","chr11": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 150945795 61734933 .. .. .. .. .. .. .. ..@ width : int [1:2] 46 151 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "SMARCD3" "FTH1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "TCAGTGCAGGAATGCGGCAGCCGCGGCGGCGGCGGCGGCGGCGGG" "GGCTGCGCGGCGCTGGAGCGGCGGCGGGGGCCTTGGGGCAGTCCGAGGGTGCGGTGAAGAGGTGACGGAGGGCTGGCTATGGGCGGCCGGCCGGGGTGGGGAACGAGCGCCGGGTTCCGTCCAAGCA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr7" "chr11" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "36" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "ATP5A1->RP5-857K21.4" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr18","chr1": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 43671427 569767 .. .. .. .. .. .. .. ..@ width : int [1:2] 234 228 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "ATP5A1" "RP5-857K21.4" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GGGCTTTCAGACCAACTCGCCTACGCGTCTTGGAACCAATTGGACCCTTTCCATCAATAGCATTACCAAGGGCATCAACTACACGACCCAACAGCTCCTCACCAACTGGAACGTCCACAATGGCTCC"| __truncated__ "ATCACATGCCTATCATATAGTAAAACCCAGCCCATGGCCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCACAACCCTCCTCATACTAGGC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr18" "chr1" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "39" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "KRT8->KRT7" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chr12": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 53295651 52627363 .. .. .. .. .. .. .. ..@ width : int [1:2] 189 171 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 1 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "KRT8" "KRT7" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCGGCTATGGTGGGGCCAGCGGCATGGGAGGCATCACCGCAGTTACGGTCAACCAGAGCCTGCTGAGCCCCCTTGTCCTGGAGGTGGACCCCAACATCCAGGCCGTGCGCACCCAGGAGAAGGAGCA"| __truncated__ "ATCAAGACCCTCAACAACAAGTTTGCCTCCTTCATCGACAAGGTGCGGTTTCTGGAGCAGCAGAACAAGCTGCTGGAGACCAAGTGGACGCTGCTGCAGGAGCAGAAGTCGGCCAAGAGCAGCCGCC"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chr12" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "2116" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MAFIP->SLCO5A1" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 2 levels "chr21","chr8": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 9826628 70602287 .. .. .. .. .. .. .. ..@ width : int [1:2] 282 185 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 2 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MAFIP" "SLCO5A1" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "CCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTA"| __truncated__ "CGGGGGGGCGCCAGGGGCCTCCCACTTATTCTACACCTCTCATGTCTCTTCACCATGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGT"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:2] "chr21" "chr8" .. .. .. .. .. .. .. ..@ seqlengths : int [1:2] NA NA .. .. .. .. .. .. .. ..@ is_circular: logi [1:2] NA NA .. .. .. .. .. .. .. ..@ genome : chr [1:2] NA NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() $ :Formal class 'fSet' [package "chimera"] with 4 slots .. ..@ fusionInfo:List of 7 .. .. ..$ fusionTool : chr "deFuse" .. .. ..$ UniqueCuttingPositionCount: chr "0" .. .. ..$ SeedCount : chr "40" .. .. ..$ RescuedCount : chr "0" .. .. ..$ SplicePattern : chr "-" .. .. ..$ FusionGene : chr "MT-ND1->MT-ND6" .. .. ..$ frameShift : chr "-" .. ..@ fusionLoc :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 1 level "chrMT": 1 .. .. .. .. .. .. .. ..@ lengths : int 2 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:2] 3870 14450 .. .. .. .. .. .. .. ..@ width : int [1:2] 189 203 .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 .. .. .. .. .. .. .. ..@ lengths : int [1:2] 1 1 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ KnownGene : chr [1:2] "MT-ND1" "MT-ND6" .. .. .. .. .. .. .. .. ..$ KnownTranscript : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownExonNumber : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ KnownTranscriptStrand : logi [1:2] NA NA .. .. .. .. .. .. .. .. ..$ FusionJunctionSequence: chr [1:2] "GCTGGAGATTGTAATGGGTATGGAGACATATCATATAAGTAATGCTAGGGTGAGTGGTAGGAAGTTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCAT"| __truncated__ "TTGAGGAGTATCCTGAGGCATGGGGGTCAGGGGTTGAGGTCTTGGTGAGTGTTTTAGTGGGGTTAGCGATGGAGGTAGGATTGGTGCTGTGGGTGAAAGAGTATGATGGGGTGGTGGTTGTGGTAAA"| __truncated__ .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr "chrMT" .. .. .. .. .. .. .. ..@ seqlengths : int NA .. .. .. .. .. .. .. ..@ is_circular: logi NA .. .. .. .. .. .. .. ..@ genome : chr NA .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 2 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. ..@ end : int [1:2] 1 2 .. .. .. .. .. ..@ NAMES : chr [1:2] "gene1" "gene2" .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "GRanges" .. .. .. ..@ metadata : list() .. ..@ fusionRNA :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. .. ..@ pool :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots .. .. .. .. .. ..@ xp_list : list() .. .. .. .. .. ..@ .link_to_cached_object_list: list() .. .. .. ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots .. .. .. .. .. ..@ group : int(0) .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementType : chr "DNAString" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..@ fusionGA :Formal class 'GAlignments' [package "GenomicAlignments"] with 8 slots .. .. .. ..@ NAMES : NULL .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ start : int(0) .. .. .. ..@ cigar : chr(0) .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. ..@ genome : chr(0) .. .. .. ..@ metadata : list() [list output truncated]

Examples

data(df.e)
## maybe str(df.e) ; plot(df.e) ...

yhoogstrate/FuMaR documentation built on May 4, 2019, 2:33 p.m.