Reads the linx.breakend.tsv file.
Examples
x <- system.file("extdata/tables/subject_a.tumor.linx.breakend.tsv", package = "linxreport")
(l <- linx_breakend_read(x))
#> # A tibble: 20 × 22
#> id svId vcfId coords isStart gene transcriptId canonical geneOrientation
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 0 0 0 chr9:… true MLLT3 ENST0000038… true Downstream
#> 2 1 0 0 chr9:… true MIR4… ENST0000058… true Downstream
#> 3 2 0 0 chr9:… true RNU4… ENST0000041… true Upstream
#> 4 3 0 2 chr11… false KMT2A ENST0000053… true Upstream
#> 5 4 0 2 chr11… false TTC36 ENST0000030… true Upstream
#> 6 5 0 2 chr11… false TMEM… ENST0000031… true Upstream
#> 7 6 0 2 chr11… false RPL5… ENST0000046… true Upstream
#> 8 7 0 2 chr11… false ARCN1 ENST0000026… true Upstream
#> 9 8 1 1 chr9:… true MLLT3 ENST0000038… true Upstream
#> 10 9 1 1 chr9:… true MIR4… ENST0000058… true Upstream
#> 11 10 1 1 chr9:… true RNU4… ENST0000041… true Downstream
#> 12 11 1 3 chr11… false KMT2A ENST0000053… true Downstream
#> 13 12 1 3 chr11… false TTC36 ENST0000030… true Downstream
#> 14 13 1 3 chr11… false TMEM… ENST0000031… true Downstream
#> 15 14 1 3 chr11… false RPL5… ENST0000046… true Downstream
#> 16 15 1 3 chr11… false ARCN1 ENST0000026… true Downstream
#> 17 16 2 4 chr19… true C19o… ENST0000032… true Downstream
#> 18 17 2 4 chr19… true CCNE1 ENST0000026… true Upstream
#> 19 18 3 5 chr19… true C19o… ENST0000032… true Upstream
#> 20 19 3 5 chr19… true CCNE1 ENST0000026… true Downstream
#> # ℹ 13 more variables: disruptive <chr>, reportedStatus <chr>,
#> # undisruptedCopyNumber <dbl>, regionType <chr>, codingType <chr>,
#> # biotype <chr>, exonicBasePhase <dbl>, nextSpliceExonRank <dbl>,
#> # nextSpliceExonPhase <dbl>, nextSpliceDistance <dbl>, totalExonCount <dbl>,
#> # exonUp <dbl>, exonDown <dbl>