Extract mutations.

Getter to obtain mutation calls from an object.

Mutations(x, cna = c("clonal", "subclonal"), type = c("SNV", "indel"))

Arguments

x

A CNAqc object.

cna

"clonal" for clonal CNAs, "subclonal" for subclonal CNAs.

type

"SNV" for single-nucleotide variants, "indel" for insertion-deletions.

Value

A tibble with the data.

Examples

data("example_PCAWG", package = 'CNAqc')
Mutations(example_PCAWG)
#> # A tibble: 293,736 × 60
#>    chr        from        to ref   alt      NV    DP    VAF sample icgc_donor_id
#>    <chr>     <dbl>     <dbl> <chr> <chr> <dbl> <dbl>  <dbl> <chr>  <chr>        
#>  1 chr1  149665366 149665366 G     A        71   320 0.222  51893… DO220903     
#>  2 chr1  149672877 149672877 C     T        28   116 0.241  51893… DO220903     
#>  3 chr1  149684625 149684625 C     T         9   151 0.0596 51893… DO220903     
#>  4 chr1  149691693 149691693 G     A        57   175 0.326  51893… DO220903     
#>  5 chr1  149703118 149703118 G     A        17   120 0.142  51893… DO220903     
#>  6 chr1  149705313 149705313 C     T        63   147 0.429  51893… DO220903     
#>  7 chr1  149718385 149718385 G     A        48   187 0.257  51893… DO220903     
#>  8 chr1  149722228 149722228 G     A        79   133 0.594  51893… DO220903     
#>  9 chr1  149729318 149729318 G     A        10   165 0.0606 51893… DO220903     
#> 10 chr1  149730287 149730287 T     A        53   259 0.205  51893… DO220903     
#> # ℹ 293,726 more rows
#> # ℹ 50 more variables: project_code <chr>, icgc_specimen_id <chr>,
#> #   icgc_sample_id <chr>, submitted_sample_id <chr>,
#> #   submitted_matched_sample_id <chr>, chromosome_strand <dbl>,
#> #   assembly_version <chr>, mutation_type <chr>, reference_genome_allele <chr>,
#> #   quality_score <lgl>, probability <lgl>, verification_status <chr>,
#> #   verification_platform <lgl>, biological_validation_status <chr>, …