Extract drivers data.

Returns a tibble with the drivers annotated on certain chromosomes, extracting VAF or CCF values (if computed). If drivers are not annotated NULL is returned.

get_drivers(x, chromosomes = paste0("chr", c(1:22, "X", "Y")), which = "VAF")

Arguments

x

A CNAqc object.

chromosomes

Which chromosomes to subset.

which

A keyword for "VAF" or "CCF".

Value

A tibble

Examples

data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)
#> 
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#> 
#> ℹ Using reference genome coordinates for: GRCh38.
#> ✔ Found annotated driver mutations: TTN, CTCF, and TP53.
#> ✔ Fortified calls for 12963 somatic mutations: 12963 SNVs (100%) and 0 indels.
#> ! CNAs have no CCF, assuming clonal CNAs (CCF = 1).
#> ✔ Fortified CNAs for 267 segments: 267 clonal and 0 subclonal.
#> ✔ 12963 mutations mapped to clonal CNAs.

get_drivers(x)
#> # A tibble: 3 × 16
#>   chr        from       to ref   alt   FILTER    DP    NV   VAF ANNOVAR_FUNCTION
#>   <chr>     <dbl>    <dbl> <chr> <chr> <chr>  <dbl> <dbl> <dbl> <chr>           
#> 1 chr2  179431633   1.79e8 C     T     PASS     117    77 0.658 exonic          
#> 2 chr16  67646006   6.76e7 C     T     PASS     120    54 0.45  exonic          
#> 3 chr17   7577106   7.58e6 G     C     PASS      84    78 0.929 exonic          
#> # ℹ 6 more variables: GENE <chr>, is_driver <lgl>, driver_label <chr>,
#> #   type <chr>, karyotype <chr>, segment_id <chr>