Processes the purple.cnv.germline.tsv file.
and selects columns of interest.
Value
List with two elements:
tab: Tibble with more condensed columns.descr: Description of tibble columns.
Examples
x <- system.file("extdata/purple/purple.cnv.germline.tsv", package = "gpgr")
(pp <- purple_cnv_germ_process(x))
#> $tab
#> # A tibble: 67 × 9
#> Chr Start End CN `CN Min+Maj` `Start/End SegSupport` Method
#> <fct> <int> <int> <dbl> <chr> <chr> <chr>
#> 1 chr1 7510001 7511000 0 0+0 NONE-UNKNOWN GERMLINE…
#> 2 chr1 14110001 14113000 0.4 0+0.4 NONE-UNKNOWN GERMLINE…
#> 3 chr1 15825001 15829000 0.4 0+0.3 NONE-UNKNOWN GERMLINE…
#> 4 chr1 58278001 58279000 0.3 0+0.3 NONE-UNKNOWN GERMLINE…
#> 5 chr1 61617001 61618000 0.1 0+0.1 NONE-UNKNOWN GERMLINE…
#> 6 chr1 79756001 79757000 0 0+0 NONE-UNKNOWN GERMLINE…
#> 7 chr1 85935001 85939000 0.2 0+0.2 NONE-UNKNOWN GERMLINE…
#> 8 chr1 89010001 89013000 0.1 0+0.1 NONE-UNKNOWN GERMLINE…
#> 9 chr1 105473001 105481000 0.1 0+0.1 NONE-UNKNOWN GERMLINE…
#> 10 chr1 110834001 110845000 0 0+0 NONE-UNKNOWN GERMLINE…
#> # ℹ 57 more rows
#> # ℹ 2 more variables: `BAF (count)` <chr>, `GC (windowCount)` <chr>
#>
#> $descr
#> # A tibble: 7 × 2
#> Column Description
#> <chr> <chr>
#> 1 Chr/Start/End Coordinates of copy number segment
#> 2 CN Fitted absolute copy number of segment adjusted for puri…
#> 3 CN Min+Maj CopyNumber of minor + major allele adjusted for purity
#> 4 Start/End SegSupport Type of SV support for the CN breakpoint at start/end of…
#> 5 Method Method used to determine the CN of the region. Allowed v…
#> 6 BAF (count) Tumor BAF after adjusted for purity and ploidy (Count of…
#> 7 GC (windowCount) Proportion of segment that is G or C (Count of COBALT wi…
#>