Split a CNAqc object by chromosome, returning a named list with data splits by chromosomes. In this way it is easy to run QC steps per chromosome.
An object created by CNAqc.
A list of chromosomes to retain.
A named list of CNAqc objects.
data("example_PCAWG", package = 'CNAqc')
# Split of tje PCAWG object, for instance
split_by_chromosome(example_PCAWG)
#>
#> ── chr1
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 11027 somatic mutations: 10983 SNVs (100%) and 44 indels.
#> ✔ Fortified CNAs for 40 segments: 40 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 11027 mutations mapped to clonal CNAs.
#>
#> ── chr2
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 29957 somatic mutations: 29857 SNVs (100%) and 100 indels.
#> ✔ Fortified CNAs for 13 segments: 13 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 29957 mutations mapped to clonal CNAs.
#>
#> ── chr3
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 26192 somatic mutations: 26103 SNVs (100%) and 89 indels.
#> ✔ Fortified CNAs for 17 segments: 17 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 26192 mutations mapped to clonal CNAs.
#>
#> ── chr4
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 21187 somatic mutations: 21104 SNVs (100%) and 83 indels.
#> ✔ Fortified CNAs for 377 segments: 377 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 21179 mutations mapped to clonal CNAs.
#>
#> ── chr5
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 24728 somatic mutations: 24624 SNVs (100%) and 104 indels.
#> ✔ Fortified CNAs for 14 segments: 14 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 24728 mutations mapped to clonal CNAs.
#>
#> ── chr6
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 19446 somatic mutations: 19383 SNVs (100%) and 63 indels.
#> ✔ Fortified CNAs for 14 segments: 14 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 19035 mutations mapped to clonal CNAs.
#>
#> ── chr7
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Found annotated driver mutations: BRAF.
#> ✔ Fortified calls for 21030 somatic mutations: 20955 SNVs (100%) and 75 indels.
#> ✔ Fortified CNAs for 17 segments: 17 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 21030 mutations mapped to clonal CNAs.
#>
#> ── chr8
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 19332 somatic mutations: 19270 SNVs (100%) and 62 indels.
#> ✔ Fortified CNAs for 62 segments: 62 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 19308 mutations mapped to clonal CNAs.
#>
#> ── chr9
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Found annotated driver mutations: CDKN2A.
#> ✔ Fortified calls for 7122 somatic mutations: 7101 SNVs (100%) and 21 indels.
#> ✔ Fortified CNAs for 7 segments: 7 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 7122 mutations mapped to clonal CNAs.
#>
#> ── chr10
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 5065 somatic mutations: 5052 SNVs (100%) and 13 indels.
#> ✔ Fortified CNAs for 19 segments: 19 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 5065 mutations mapped to clonal CNAs.
#>
#> ── chr12
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 14351 somatic mutations: 14287 SNVs (100%) and 64 indels.
#> ✔ Fortified CNAs for 4 segments: 4 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 14351 mutations mapped to clonal CNAs.
#>
#> ── chr13
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 8024 somatic mutations: 7986 SNVs (100%) and 38 indels.
#> ✔ Fortified CNAs for 7 segments: 7 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 8024 mutations mapped to clonal CNAs.
#>
#> ── chr14
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 11085 somatic mutations: 11041 SNVs (100%) and 44 indels.
#> ✔ Fortified CNAs for 1 segments: 1 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 11085 mutations mapped to clonal CNAs.
#>
#> ── chr15
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 8566 somatic mutations: 8536 SNVs (100%) and 30 indels.
#> ✔ Fortified CNAs for 18 segments: 18 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 8566 mutations mapped to clonal CNAs.
#>
#> ── chr16
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 10010 somatic mutations: 9978 SNVs (100%) and 32 indels.
#> ✔ Fortified CNAs for 10 segments: 10 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 10010 mutations mapped to clonal CNAs.
#>
#> ── chr17
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Found annotated driver mutations: TP53.
#> ✔ Fortified calls for 6329 somatic mutations: 6316 SNVs (100%) and 13 indels.
#> ✔ Fortified CNAs for 8 segments: 8 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 6329 mutations mapped to clonal CNAs.
#>
#> ── chr18
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 13062 somatic mutations: 13009 SNVs (100%) and 53 indels.
#> ✔ Fortified CNAs for 9 segments: 9 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 13062 mutations mapped to clonal CNAs.
#>
#> ── chr19
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 5228 somatic mutations: 5208 SNVs (100%) and 20 indels.
#> ✔ Fortified CNAs for 9 segments: 9 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 5228 mutations mapped to clonal CNAs.
#>
#> ── chr20
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 5970 somatic mutations: 5954 SNVs (100%) and 16 indels.
#> ✔ Fortified CNAs for 2 segments: 2 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 5970 mutations mapped to clonal CNAs.
#>
#> ── chr21
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 5117 somatic mutations: 5095 SNVs (100%) and 22 indels.
#> ✔ Fortified CNAs for 2 segments: 2 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 5117 mutations mapped to clonal CNAs.
#>
#> ── chr22
#>
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: hg19.
#> ! Detected indels mutation (substitutions with >1 reference/alternative nucleotides).
#> ✔ Fortified calls for 2595 somatic mutations: 2589 SNVs (100%) and 6 indels.
#> ✔ Fortified CNAs for 4 segments: 4 clonal and 0 subclonal.
#> Warning: [CNAqc] a karyotype column is present in CNA calls, and will be overwritten
#> ✔ 2595 mutations mapped to clonal CNAs.
#> $chr1
#> ── [ CNAqc ] MySample 11027 mutations in 40 segments (40 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 2:2 [n = 7968, L = 68 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 2:1 [n = 2017, L = 19 Mb] ■■■■■■■
#> 3:2 [n = 462, L = 4 Mb] ■■
#> 3:1 [n = 428, L = 3 Mb] ■
#> 4:2 [n = 93, L = 2 Mb]
#> 3:3 [n = 24, L = 0 Mb]
#> 5:2 [n = 19, L = 0 Mb]
#> 6:2 [n = 8, L = 0 Mb]
#> 1:0 [n = 3, L = 0 Mb]
#> 7:2 [n = 3, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr2
#> ── [ CNAqc ] MySample 29957 mutations in 13 segments (13 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 3:1 [n = 29957, L = 237 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr3
#> ── [ CNAqc ] MySample 26192 mutations in 17 segments (17 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 3:2 [n = 13692, L = 104 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 2:1 [n = 12378, L = 83 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■
#> 1:0 [n = 100, L = 4 Mb]
#> 2:2 [n = 22, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 5.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr4
#> ── [ CNAqc ] MySample 21179 mutations in 377 segments (377 clonal, 0 subclonal).
#>
#> ── Clonal CNAs
#>
#> 3:1 [n = 10448, L = 67 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 3:0 [n = 8069, L = 97 Mb] ■■■■■■■■■■■■■■■■■■■■■
#> 3:2 [n = 803, L = 6 Mb] ■■
#> 3:3 [n = 801, L = 4 Mb] ■■
#> 4:3 [n = 359, L = 3 Mb] ■
#> 5:3 [n = 132, L = 1 Mb]
#> 6:3 [n = 114, L = 1 Mb]
#> 4:2 [n = 59, L = 0 Mb]
#> 10:3 [n = 56, L = 0 Mb]
#> 9:3 [n = 52, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr5
#> ── [ CNAqc ] MySample 24728 mutations in 14 segments (14 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 24592, L = 175 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 1:1 [n = 136, L = 1 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr6
#> ── [ CNAqc ] MySample 19035 mutations in 14 segments (14 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 16330, L = 122 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 2:2 [n = 2705, L = 36 Mb] ■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr7
#> ── [ CNAqc ] MySample 21030 mutations in 17 segments (17 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 3:2 [n = 21030, L = 155 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■ { BRAF }
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 5.
#>
#> ℹ There are 1 annotated driver(s) mapped to clonal CNAs.
#> chr from to ref alt DP NV VAF driver_label is_driver
#> chr7 140453136 140453136 A T 95 54 0.5684211 BRAF TRUE
#>
#> $chr8
#> ── [ CNAqc ] MySample 19308 mutations in 62 segments (62 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 3:3 [n = 9995, L = 64 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 3:2 [n = 4836, L = 27 Mb] ■■■■■■■■■■■■■
#> 2:0 [n = 3063, L = 38 Mb] ■■■■■■■■
#> 4:2 [n = 1289, L = 8 Mb] ■■■
#> 5:2 [n = 105, L = 1 Mb]
#> 6:2 [n = 20, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 6.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr9
#> ── [ CNAqc ] MySample 7122 mutations in 7 segments (7 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:0 [n = 7098, L = 114 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■ { CDKN2A }
#> 7:0 [n = 24, L = 5 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 1 annotated driver(s) mapped to clonal CNAs.
#> chr from to ref alt DP NV VAF driver_label is_driver
#> chr9 21971120 21971120 G A 23 14 0.6086957 CDKN2A TRUE
#>
#> $chr10
#> ── [ CNAqc ] MySample 5065 mutations in 19 segments (19 clonal, 0 subclonal). Ge
#>
#> ── Clonal CNAs
#>
#> 3:0 [n = 2715, L = 38 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 2:0 [n = 2287, L = 29 Mb] ■■■■■■■■■■■■■■■■■■■■■■
#> 2:1 [n = 26, L = 0 Mb]
#> 1:0 [n = 21, L = 0 Mb]
#> 4:0 [n = 15, L = 0 Mb]
#> 1:1 [n = 1, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr12
#> ── [ CNAqc ] MySample 14351 mutations in 4 segments (4 clonal, 0 subclonal). Gen
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 14351, L = 129 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr13
#> ── [ CNAqc ] MySample 8024 mutations in 7 segments (7 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:0 [n = 8024, L = 99 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr14
#> ── [ CNAqc ] MySample 11085 mutations in 1 segments (1 clonal, 0 subclonal). Gen
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 11085, L = 87 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr15
#> ── [ CNAqc ] MySample 8566 mutations in 18 segments (18 clonal, 0 subclonal). Ge
#>
#> ── Clonal CNAs
#>
#> 2:1 [n = 7617, L = 77 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 1:1 [n = 718, L = 9 Mb] ■■■
#> 3:1 [n = 146, L = 1 Mb] ■
#> 4:1 [n = 85, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 3.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr16
#> ── [ CNAqc ] MySample 10010 mutations in 10 segments (10 clonal, 0 subclonal). G
#>
#> ── Clonal CNAs
#>
#> 2:2 [n = 10002, L = 90 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 2:0 [n = 8, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr17
#> ── [ CNAqc ] MySample 6329 mutations in 8 segments (8 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 2:2 [n = 4593, L = 59 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 4:0 [n = 1732, L = 22 Mb] ■■■■■■■■■■ { TP53 }
#> 2:0 [n = 4, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 1 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
#>
#> $chr18
#> ── [ CNAqc ] MySample 13062 mutations in 9 segments (9 clonal, 0 subclonal). Gen
#>
#> ── Clonal CNAs
#>
#> 3:2 [n = 13062, L = 78 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 5.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr19
#> ── [ CNAqc ] MySample 5228 mutations in 9 segments (9 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:2 [n = 4499, L = 42 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#> 3:0 [n = 716, L = 12 Mb] ■■■■
#> 3:1 [n = 13, L = 0 Mb]
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 5.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr20
#> ── [ CNAqc ] MySample 5970 mutations in 2 segments (2 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:3 [n = 5970, L = 46 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 6.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr21
#> ── [ CNAqc ] MySample 5117 mutations in 2 segments (2 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:1 [n = 5117, L = 34 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>
#> $chr22
#> ── [ CNAqc ] MySample 2595 mutations in 4 segments (4 clonal, 0 subclonal). Geno
#>
#> ── Clonal CNAs
#>
#> 3:1 [n = 2595, L = 39 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■
#>
#> ℹ Sample Purity: 73.4% ~ Ploidy: 4.
#>
#> ℹ There are 0 annotated driver(s) mapped to clonal CNAs.
#> [1] chr from to ref alt
#> [6] DP NV VAF driver_label is_driver
#> <0 rows> (or 0-length row.names)
#>