This function extracts Cancer Cell Fractions (CCFs) estimates from a CNAqc object, after they have been computed using function `compute_CCF`. The estimates are pooled across the used karyotypes, and extracted from the `CCF_estimates` field of the input object.
CCF(x)A CNAqc object.
A mutations tibble with columns for mutation multiplicity and CCFs.
data("example_PCAWG", package = 'CNAqc')
CCF(example_PCAWG)
#> # A tibble: 120,065 × 60
#> chr from to ref alt sample icgc_donor_id project_code
#> <chr> <dbl> <dbl> <chr> <chr> <chr> <chr> <chr>
#> 1 chr1 240197260 240197260 G A 51893d3f-e7… DO220903 MELA-AU
#> 2 chr1 240197743 240197743 T - 51893d3f-e7… DO220903 MELA-AU
#> 3 chr1 240209355 240209355 G A 51893d3f-e7… DO220903 MELA-AU
#> 4 chr10 42871855 42871855 G A 51893d3f-e7… DO220903 MELA-AU
#> 5 chr10 42874161 42874161 G A 51893d3f-e7… DO220903 MELA-AU
#> 6 chr10 42886327 42886327 C T 51893d3f-e7… DO220903 MELA-AU
#> 7 chr10 42887738 42887738 G A 51893d3f-e7… DO220903 MELA-AU
#> 8 chr10 42888438 42888438 C T 51893d3f-e7… DO220903 MELA-AU
#> 9 chr10 42888486 42888486 G A 51893d3f-e7… DO220903 MELA-AU
#> 10 chr10 42891609 42891609 C T 51893d3f-e7… DO220903 MELA-AU
#> # ℹ 120,055 more rows
#> # ℹ 52 more variables: 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>, biological_validation_platform <lgl>, …