Read PURPLE CNV Somatic File

Reads the purple.cnv.somatic.tsv file, which contains the copy number profile of all (contiguous) segments of the tumor sample (see this table).

Usage

purple_cnv_som_read(x)

Arguments

x

Path to purple.cnv.somatic.tsv file.

Value

The input file as a tibble.

Examples

x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
(p <- purple_cnv_som_read(x))
#> # A tibble: 59 × 16
#>    chromosome     start       end copyNumber bafCount observedBAF   baf
#>    <chr>          <int>     <int>      <dbl>    <dbl>       <dbl> <dbl>
#>  1 chr1               1 123605522       1.02    20830       0.792 0.982
#>  2 chr1       123605523 200044314       1.99    10239       0.540 0.503
#>  3 chr1       200044315 200044570       2.83        0       0     0.649
#>  4 chr1       200044571 248956422       2.01    10341       0.540 0.505
#>  5 chr2               1  93139350       2.01    19339       0.54  0.505
#>  6 chr2        93139351 219955359       2.00    19047       0.540 0.503
#>  7 chr2       219955360 225225069       1.02     1284       0.791 0.981
#>  8 chr2       225225070 242193529       2.03     4236       0.539 0.511
#>  9 chr3               1  92214015       1.03    18629       0.792 0.983
#> 10 chr3        92214016 198295559       2.00    21114       0.539 0.504
#> # ℹ 49 more rows
#> # ℹ 9 more variables: segmentStartSupport <chr>, segmentEndSupport <chr>,
#> #   method <chr>, depthWindowCount <int>, gcContent <dbl>, minStart <int>,
#> #   maxStart <int>, minorAlleleCopyNumber <dbl>, majorAlleleCopyNumber <dbl>