Example PCAWG tumour
data(example_PCAWG)A CNAqc object created for a PCAWG sample, with subclonal CNAs called by Battenberg.
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). https://doi.org/10.1038/s41586-020-1969-6
data(example_PCAWG)
example_PCAWG
#> ── [ CNAqc ] 293736 mutations in 667 segments (654 clonal, 13 subclonal). Genom
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 88422, L = 692 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 3:2 [n = 58384, L = 417 Mb] ■■■■■■■■■■■■■■■■■■ { BRAF }
#> 3:1 [n = 48704, L = 380 Mb] ■■■■■■■■■■■■■■■
#> 3:0 [n = 26622, L = 360 Mb] ■■■■■■■■ { CDKN2A }
#> 2:2 [n = 25290, L = 253 Mb] ■■■■■■■■
#> 3:3 [n = 16790, L = 115 Mb] ■■■■■
#> 2:0 [n = 5374, L = 67 Mb] ■■
#> 4:0 [n = 1752, L = 22 Mb] ■ { TP53 }
#> 4:2 [n = 1441, L = 11 Mb]
#> 1:1 [n = 855, L = 9 Mb]
#>
#>
#> ── Subclonal CNAs (showing up to 10 segments)
#>
#> chr11@55700000 [n = 10468, L = 78.75 Mb] 2:1 (0.21) 2:2 (0.79) ■■■■■■■■■■
#> chr11@17365005 [n = 5389, L = 31.55 Mb] 2:1 (0.21) 2:2 (0.79) ■■■■■
#> chr11@5372292 [n = 1014, L = 11.99 Mb] 2:1 (0.21) 2:2 (0.79)
#> chr11@202253 [n = 610, L = 5.17 Mb] 2:1 (0.22) 2:2 (0.78)
#> chr11@48918601 [n = 542, L = 2.68 Mb] 2:1 (0.25) 2:2 (0.75)
#> chr6@82432583 [n = 301, L = 1.81 Mb] 2:1 (0.19) 2:2 (0.81)
#> chr11@51600000 [n = 290, L = 4.1 Mb] 2:1 (0.26) 2:2 (0.74)
#> chr6@81896364 [n = 69, L = 0.54 Mb] 2:1 (0.19) 2:2 (0.81)
#> chr6@93956180 [n = 41, L = 0.11 Mb] 2:1 (0.2) 2:2 (0.8)
#> chr8@42633277 [n = 13, L = 0.26 Mb] 2:1 (0.28) 2:2 (0.72)
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 3 annotated driver(s) mapped to clonal CNAs.
#> chr from to ref alt DP NV VAF driver_label is_driver
#> chr17 7577082 7577082 C T 78 70 0.8974359 TP53 TRUE
#> chr7 140453136 140453136 A T 95 54 0.5684211 BRAF TRUE
#> chr9 21971120 21971120 G A 23 14 0.6086957 CDKN2A TRUE
#>
#> ── PASS Peaks QC closest: 199%, λ = 0.0059. Purity correction: 1%. ───────────
#>
#> ℹ 2:1 ~ n = 88422 ( 74%) → PASS 0.01 PASS -0.006
#> ℹ 2:2 ~ n = 25290 ( 21%) → PASS 0.01 PASS 0.002
#> ℹ 2:0 ~ n = 5374 ( 4%) → PASS 0.015 PASS -0.001
#> ℹ 1:1 ~ n = 855 (0.7%) → PASS -0.006
#> ℹ 1:0 ~ n = 124 (0.1%) → PASS 0.008
#>
#> ── General peak QC (154430 mutations): PASS 27 FAIL 13 - epsilon = 0.05. ───
#>
#> ℹ 3:0 ~ n = 26622 ( 17%) → PASS 3 FAIL 0
#> ℹ 3:1 ~ n = 48704 ( 32%) → PASS 3 FAIL 0
#> ℹ 3:2 ~ n = 58384 ( 38%) → PASS 3 FAIL 0
#> ℹ 3:3 ~ n = 16790 ( 11%) → PASS 3 FAIL 0
#> ℹ 4:2 ~ n = 1441 ( 1%) → PASS 3 FAIL 1
#> ℹ 4:3 ~ n = 359 ( 0%) → PASS 3 FAIL 1
#> ℹ 5:3 ~ n = 132 ( 0%) → PASS 3 FAIL 2
#> ℹ 4:0 ~ n = 1752 ( 1%) → PASS 2 FAIL 2
#> ℹ 5:2 ~ n = 132 ( 0%) → PASS 2 FAIL 3
#> ℹ 6:3 ~ n = 114 ( 0%) → PASS 2 FAIL 4
#>
#> ── Subclonal peaks QC (7 segments, initial state 2:1): linear 5 branching 0 eith
#>
#> ── PASS Linear models
#> ℹ chr11@17365005 ~ (31.6Mb, n = 5389) 2:1 (21) + 2:2 (79) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]
#> ℹ chr11@202253 ~ (5.2Mb, n = 610) 2:1 (22) + 2:2 (78) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]
#> ℹ chr11@51600000 ~ (4.1Mb, n = 290) 2:1 (26) + 2:2 (74) : A1B1 -> A1A2B1 -> A1A2B1B2 [75]
#> ℹ chr11@5372292 ~ (12Mb, n = 1014) 2:1 (21) + 2:2 (79) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]
#> ℹ chr11@55700000 ~ (78.8Mb, n = 10468) 2:1 (21) + 2:2 (79) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]
#>
#> ── UNKNOWN Either branching or linear models
#> ℹ chr11@48918601 ~ (2.7Mb, n = 542) 2:1 (25) + 2:2 (75) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]; A1B1 -> A1A2B1 | A1A2B1B2 [100]; A1B1 -> A1A2B1B2 -> A2B1B2 [100]
#> ℹ chr6@82432583 ~ (1.8Mb, n = 301) 2:1 (19) + 2:2 (81) : A1B1 -> A1A2B1 -> A1A2B1B2 [100]; A1B1 -> A1A2B1 | A1A2B1B2 [100]; A1B1 -> A1A2B1B2 -> A2B1B2 [100]
#>
#> ✔ Cancer Cell Fraction (CCF) data available for karyotypes:1:0, 1:1, 2:0, 2:1, and 2:2.
#> ✔ PASS CCF via ENTROPY.
#> ✔ PASS CCF via ENTROPY.
#> ✔ PASS CCF via ENTROPY.
#> ✔ PASS CCF via ENTROPY.
#> ✔ PASS CCF via ENTROPY.