Read LINX Fusion File

Reads the linx.fusion.tsv file.

Usage

linx_fusion_read(x)

Arguments

x

Path to linx.fusion.tsv file.

Value

The input file as a tibble.

Examples

x <- system.file("extdata/tables/COLO829v003T.linx.fusion.tsv", package = "linxreport")
(l <- linx_fusion_read(x))
#> # A tibble: 13 × 24
#>    fivePrimeBreakendId threePrimeBreakendId name           reported reportedType
#>    <chr>               <chr>                <chr>          <chr>    <chr>       
#>  1 318                 317                  DMD_DMD        false    NONE        
#>  2 330                 219                  CATSPERB_ATP1… false    NONE        
#>  3 158                 159                  ASAP1_ASAP1    false    NONE        
#>  4 240                 243                  OIP5_OIP5      false    NONE        
#>  5 331                 175                  RARB_BICC1     false    NONE        
#>  6 305                 306                  GOLGA6L2_ARHG… false    NONE        
#>  7 332                 208                  RARB_TRHDE     false    NONE        
#>  8 184                 187                  PTEN_PTEN      false    NONE        
#>  9 129                 128                  MAGI2_MAGI2    false    NONE        
#> 10 333                 334                  ITIH5_TXNDC2   false    NONE        
#> 11 315                 314                  LARGE1_LARGE1  false    NONE        
#> 12 275                 335                  ANKLE1_MRPL34  false    NONE        
#> 13 6                   4                    NOTCH2NLC_NOT… false    NONE        
#> # ℹ 19 more variables: reportableReasons <chr>, phased <chr>, likelihood <chr>,
#> #   chainLength <dbl>, chainLinks <dbl>, chainTerminated <chr>,
#> #   domainsKept <chr>, domainsLost <chr>, skippedExonsUp <dbl>,
#> #   skippedExonsDown <dbl>, fusedExonUp <dbl>, fusedExonDown <dbl>,
#> #   geneStart <chr>, geneContextStart <chr>, transcriptStart <chr>,
#> #   geneEnd <chr>, geneContextEnd <chr>, transcriptEnd <chr>,
#> #   junctionCopyNumber <dbl>