R/subsample.R
subset_by_segment_minmutations.RdIt retains only the set of clonal segments that have mapped at least `n` mutations mapped.
subset_by_segment_minmutations(x, n = 50)A CNAqc object that should have less segments.
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.
subset_by_segment_minmutations(x, 0)
#> ! This filter has no effect on the input data.
#> ── [ CNAqc ] MySample 12963 mutations in 267 segments (267 clonal, 0 subclonal).
#>
#> ── Clonal CNAs
#>
#> 2:2 [n = 7478, L = 1483 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■ { CTCF }
#> 4:2 [n = 1893, L = 331 Mb] ■■■■■■■
#> 3:2 [n = 1625, L = 357 Mb] ■■■■■■
#> 2:1 [n = 1563, L = 420 Mb] ■■■■■■ { TTN }
#> 3:0 [n = 312, L = 137 Mb] ■
#> 2:0 [n = 81, L = 39 Mb] { TP53 }
#> 16:2 [n = 4, L = 0 Mb]
#> 25:2 [n = 2, L = 1 Mb]
#> 3:1 [n = 2, L = 1 Mb]
#> 106:1 [n = 1, L = 0 Mb]
#>
#> ℹ Sample Purity: 89% ~ Ploidy: 4.
#>
#> ℹ There are 3 annotated driver(s) mapped to clonal CNAs.
#> chr from to ref alt DP NV VAF driver_label is_driver
#> chr2 179431633 179431634 C T 117 77 0.6581197 TTN TRUE
#> chr16 67646006 67646007 C T 120 54 0.4500000 CTCF TRUE
#> chr17 7577106 7577107 G C 84 78 0.9285714 TP53 TRUE
subset_by_segment_minmutations(x, 10)
#> ℹ Dropping 79 clonal segments with less than 10 mutations - losing 272/12963 mutations (2.0982797192008%)
#>
#> ── 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.
#> ✔ Fortified CNAs for 147 segments: 147 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 12691 mutations mapped to clonal CNAs.
#>
#> ┌ Driver(s): TP53 ─────────────────────────────────┐
#> │ │
#> │ Driver cannot be mapped - out of any segment! │
#> │ │
#> └───────────────────────────────────────────────────┘
#> ── [ CNAqc ] MySample 12691 mutations in 147 segments (147 clonal, 0 subclonal).
#>
#> ── Clonal CNAs
#>
#> 2:2 [n = 7399, L = 1452 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■ { CTCF }
#> 4:2 [n = 1874, L = 327 Mb] ■■■■■■■
#> 3:2 [n = 1537, L = 321 Mb] ■■■■■■
#> 2:1 [n = 1510, L = 400 Mb] ■■■■■ { TTN }
#> 3:0 [n = 311, L = 136 Mb] ■
#> 2:0 [n = 60, L = 26 Mb]
#>
#> ℹ Sample Purity: 89% ~ Ploidy: 4.
#>
#> ℹ There are 2 annotated driver(s) mapped to clonal CNAs.
#> chr from to ref alt DP NV VAF driver_label is_driver
#> chr2 179431633 179431634 C T 117 77 0.6581197 TTN TRUE
#> chr16 67646006 67646007 C T 120 54 0.4500000 CTCF TRUE