Processes the purple.cnv.somatic.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.somatic.tsv", package = "gpgr")
(pp <- purple_cnv_som_process(x))
#> $tab
#> # A tibble: 59 × 9
#> Chr Start End CN `CN Min+Maj` `Start/End SegSupport` Method
#> <fct> <int> <int> <dbl> <chr> <chr> <chr>
#> 1 chr1 1 123605522 1 0+1 TELOMERE-CENTROMERE BAF_WEIG…
#> 2 chr1 123605523 200044314 2 1+1 CENTROMERE-DUP BAF_WEIG…
#> 3 chr1 200044315 200044570 2.8 1+1.8 DUP-DUP STRUCTUR…
#> 4 chr1 200044571 248956422 2 1+1 DUP-TELOMERE BAF_WEIG…
#> 5 chr2 1 93139350 2 1+1 TELOMERE-CENTROMERE BAF_WEIG…
#> 6 chr2 93139351 219955359 2 1+1 CENTROMERE-BND BAF_WEIG…
#> 7 chr2 219955360 225225069 1 0+1 BND-BND BAF_WEIG…
#> 8 chr2 225225070 242193529 2 1+1 BND-TELOMERE BAF_WEIG…
#> 9 chr3 1 92214015 1 0+1 TELOMERE-CENTROMERE BAF_WEIG…
#> 10 chr3 92214016 198295559 2 1+1 CENTROMERE-TELOMERE BAF_WEIG…
#> # ℹ 49 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…
#>