Getter to obtain mutation calls from an object.
A CNAqc object.
"clonal" for clonal CNAs, "subclonal" for subclonal CNAs.
"SNV" for single-nucleotide variants, "indel" for insertion-deletions.
A tibble with the data.
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>, …