Read LINX Links File

Reads the linx.links.tsv file.

Usage

linx_links_read(x)

Arguments

x

Path to linx.links.tsv file.

Value

The input file as a tibble.

Examples

x <- system.file("extdata/tables/COLO829v003T.linx.links.tsv", package = "linxreport")
(l <- linx_links_read(x))
#> # A tibble: 27 × 17
#>    clusterId chainId chainIndex chainCount lowerSvId upperSvId
#>    <chr>     <chr>   <chr>           <dbl> <chr>     <chr>    
#>  1 2         0       0                   3 96        97       
#>  2 2         0       1                   3 96        98       
#>  3 11        0       0                   2 78        80       
#>  4 14        0       0                   2 84        85       
#>  5 16        0       0                   5 87        88       
#>  6 16        0       1                   5 91        88       
#>  7 16        0       2                   5 91        92       
#>  8 16        0       3                   5 92        93       
#>  9 27        0       0                   2 147       146      
#> 10 25        0       0                   4 23        109      
#> # ℹ 17 more rows
#> # ℹ 11 more variables: lowerBreakendIsStart <chr>, upperBreakendIsStart <chr>,
#> #   chromosome <chr>, arm <chr>, assembled <chr>, traversedSVCount <dbl>,
#> #   length <dbl>, junctionCopyNumber <dbl>,
#> #   junctionCopyNumberUncertainty <dbl>, pseudogeneInfo <chr>, ecDna <chr>