Getter to obtain copy number calls from an object.
CNA(x, type = c("clonal", "subclonal"))A CNAqc object.
"clonal" for clonal CNAs, "subclonal" for subclonal CNAs.
A tibble with the data.
data("example_PCAWG", package = 'CNAqc')
CNA(example_PCAWG)
#> # A tibble: 667 × 17
#> chr from to Major Major_2 minor minor_2 CCF length segment_id n
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <int>
#> 1 chr1 1 e0 8.22e5 4 NA 2 NA 1 8.22e5 chr1:1:82… NA
#> 2 chr1 1.50e8 1.51e8 4 NA 2 NA 1 1.32e6 chr1:1496… 39
#> 3 chr1 1.51e8 1.51e8 6 NA 2 NA 1 1.65e4 chr1:1509… NA
#> 4 chr1 1.51e8 1.51e8 7 NA 2 NA 1 8.08e3 chr1:1509… 1
#> 5 chr1 1.51e8 1.51e8 7 NA 2 NA 1 1.80e4 chr1:1509… 2
#> 6 chr1 1.51e8 1.52e8 5 NA 2 NA 1 4.58e5 chr1:1511… 17
#> 7 chr1 1.52e8 1.52e8 6 NA 2 NA 1 1.64e5 chr1:1515… 8
#> 8 chr1 1.52e8 1.52e8 5 NA 2 NA 1 6.72e3 chr1:1517… 2
#> 9 chr1 1.53e8 1.53e8 4 NA 2 NA 1 1.23e5 chr1:1527… 12
#> 10 chr1 1.53e8 1.53e8 4 NA 0 NA 1 2.78e4 chr1:1529… 2
#> # ℹ 657 more rows
#> # ℹ 6 more variables: QC_PASS <lgl>, matched <int>, karyotype <chr>,
#> # karyotype_2 <chr>, analysed <lgl>, mutations <list>