Closed ahorn720 closed 3 years ago
after some further digging I believe I've found where the issue is occurring.
the if/then statements within compute_CCF
lead to mutmult_two_copies_entropy
where at lines 14 and 15 a couple values aren't made...which are then put into the dbinom function which of course won't work without those values.
> x
── [ CNAqc ] n = 125 mutations in 237 segments (237 clonal + 0 subclonal). Genome reference: hg38. ───────────────────
2:0 [n = 125, L = 178 Mb] ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■
ℹ Sample Purity: 80.5% ~ Ploidy: 2.
> karyotype
[1] "2:0"
> cli::cli_rule("Computing mutation multiplicity for karyotype {.field {karyotype}} using the entropy method.")
── Computing mutation multiplicity for karyotype 2:0 using the entropy method. ────────────────────────────────────────
> A = as.numeric(strsplit(karyotype, ":")[[1]][1])
> B = as.numeric(strsplit(karyotype, ":")[[1]][2])
> cl_seg = x$cna %>% dplyr::filter(CCF == 1) %>% dplyr::pull(segment_id)
> snvs_k = x$snvs %>% dplyr::filter(karyotype == !!karyotype,
+ segment_id %in% cl_seg)
> expectation = CNAqc:::expected_vaf_peak(A, B, x$purity) %>%
+ mutate(label = ifelse(mutation_multiplicity == 1, "One copy",
+ "Two copies"))
> med_coverage = median(snvs_k$DP, na.rm = TRUE)
> cli::cli_alert_info("Expected Binomial peak(s) for these calls (1 and 2 copies): {.value {expectation$peak}}")
ℹ Expected Binomial peak(s) for these calls (1 and 2 copies):
Warning message:
Unknown or uninitialised column: `peak`.
> p_1 = expectation$peak[1]
Warning message:
Unknown or uninitialised column: `peak`.
> p_2 = expectation$peak[2]
Warning message:
Unknown or uninitialised column: `peak`.
the table expectation
actually looks like this:
> expectation
# A tibble: 2 x 5
mutation_multiplicity karyotype peak.Purity peak.Purity.1 label
<dbl> <chr> <dbl> <dbl> <chr>
1 1 2:0 0.402 0.805 One copy
2 2 2:0 0.402 0.805 Two copies
so maybe it needs to have the column names renamed or something like that.
Just thought I'd ping this comment in case it was forgotten. Thank you in advance for spending the time to work on this
Hi @ahorn720 thanks for pointing this out
We'll have a look
Well this is interesting thanks @ahorn720 . I can definitely debug this for you and I am sure it must be some simple type of error. Is there any chance you could share with me the object x
you pass to CNAqc ccf = compute_CCF(x)
? In theory I do not all the muts, but maybe only those that generate the error (also you can anonimise your data any way you like).
certainly peak.Purity.1
should not be there, but I need to run it line-by-line to see where that comes out from - it might be some change in the underlying managment of tibble names by tidyverse
packages.
I can say that running it on several different datasets over the last few weeks never raised this error to me, so I presume is something really simple to fix (maybe some NA where there should be none).
Hi Caravagn! Sure thing. Here is a reprex::reprex of the first issue I ran into which led me to that bug.
library(CNAqc)
#> ✓ Loading CNAqc, 'Copy Number Alteration quality check'. Support : <https://caravagn.github.io/CNAqc/>
load("~/Desktop/cnaquestion.RData",verbose = T)
#> Loading objects:
#> snvs
#> cna
#> purity
#> ref
data.frame(snvs)
#> chr from to ref
#> 1 chr5 112740514 112740517 G
#> 2 chr5 112740524 112740526 CT
#> 3 chr5 112742073 112742074 A
#> 4 chr5 112742223 112742224 G
#> 5 chr5 112743064 112743065 A
#> 6 chr5 112745548 112745544 TTTA
#> 7 chr5 112745548 112745552 TTTA
#> 8 chr5 112745575 112745579 A
#> 9 chr5 112746162 112746163 A
#> 10 chr5 112747086 112747087 T
#> 11 chr5 112747109 112747110 A
#> 12 chr5 112748712 112748713 G
#> 13 chr5 112748724 112748725 G
#> 14 chr5 112748726 112748727 T
#> 15 chr5 112748928 112748929 A
#> 16 chr5 112749479 112749481 AT
#> 17 chr5 112749479 112749483 AT
#> 18 chr5 112749479 112749482 AT
#> 19 chr5 112749479 112749477 AT
#> 20 chr5 112749968 112749970 G
#> 21 chr5 112751050 112751051 C
#> 22 chr5 112753585 112753586 T
#> 23 chr5 112753783 112753784 T
#> 24 chr5 112758873 112758874 A
#> 25 chr5 112759356 112759358 CT
#> 26 chr5 112759356 112759354 CT
#> 27 chr5 112764078 112764075 TAAAA
#> 28 chr5 112764078 112764076 TAAAA
#> 29 chr5 112764245 112764247 CA
#> 30 chr5 112767811 112767812 G
#> 31 chr5 112768363 112768361 CA
#> 32 chr5 112768363 112768365 CA
#> 33 chr5 112768513 112768515 CT
#> 34 chr5 112769050 112769048 CTTT
#> 35 chr5 112769050 112769052 CTTT
#> 36 chr5 112769050 112769053 CTTT
#> 37 chr5 112769050 112769046 CTTT
#> 38 chr5 112771351 112771352 G
#> 39 chr5 112774464 112774466 A
#> 40 chr5 112774464 112774467 A
#> 41 chr5 112774464 112774468 A
#> 42 chr5 112775605 112775607 C
#> 43 chr5 112776137 112776138 C
#> 44 chr5 112776862 112776860 TA
#> 45 chr5 112778550 112778552 A
#> 46 chr5 112778550 112778553 A
#> 47 chr5 112778688 112778692 A
#> 48 chr5 112778834 112778835 C
#> 49 chr5 112781763 112781761 AT
#> 50 chr5 112781763 112781765 AT
#> 51 chr5 112783765 112783763 CA
#> 52 chr5 112783765 112783767 CA
#> 53 chr5 112783765 112783769 CA
#> 54 chr5 112783786 112783787 A
#> 55 chr5 112783796 112783790 GAAAGA
#> 56 chr5 112786886 112786884 CT
#> 57 chr5 112786886 112786888 CT
#> 58 chr5 112786905 112786901 TGAG
#> 59 chr5 112789691 112789692 A
#> 60 chr5 112789857 112789859 A
#> 61 chr5 112792467 112792468 C
#> 62 chr5 112794137 112794138 G
#> 63 chr5 112794389 112794390 C
#> 64 chr5 112799163 112799164 G
#> 65 chr5 112799183 112799185 C
#> 66 chr5 112800832 112800829 CAT
#> 67 chr5 112803976 112803977 C
#> 68 chr5 112804460 112804461 A
#> 69 chr5 112804461 112804462 T
#> 70 chr5 112804641 112804642 T
#> 71 chr5 112805008 112805006 TA
#> 72 chr5 112805530 112805531 T
#> 73 chr5 112806552 112806557 CTTTATTTA
#> 74 chr5 112806552 112806543 CTTTATTTA
#> 75 chr5 112806552 112806547 CTTTATTTA
#> 76 chr5 112809971 112809973 T
#> 77 chr5 112813752 112813754 TA
#> 78 chr5 112813752 112813750 TA
#> 79 chr5 112815564 112815565 C
#> 80 chr5 112818847 112818849 C
#> 81 chr5 112819301 112819302 G
#> 82 chr5 112819349 112819350 G
#> 83 chr5 112820182 112820179 GACAC
#> 84 chr5 112820182 112820177 GACAC
#> 85 chr5 112821030 112821032 AT
#> 86 chr5 112821030 112821028 AT
#> 87 chr5 112826600 112826597 AAC
#> 88 chr5 112828001 112828002 C
#> 89 chr5 112828457 112828455 TAA
#> 90 chr5 112828457 112828454 TAA
#> 91 chr5 112831113 112831111 AT
#> 92 chr5 112831212 112831213 G
#> 93 chr5 112833180 112833178 ATT
#> 94 chr5 112833180 112833177 ATT
#> 95 chr5 112834238 112834236 CT
#> 96 chr5 112834257 112834252 TTTTA
#> 97 chr5 112834260 112834258 TAA
#> 98 chr5 112834261 112834262 A
#> 99 chr5 112834661 112834662 G
#> 100 chr5 112835572 112835574 AT
#> 101 chr5 112836009 112836006 CTTTTTTTTTT
#> 102 chr5 112836009 112835999 CTTTTTTTTTT
#> 103 chr5 112836165 112836163 TCC
#> 104 chr5 112836165 112836162 TCC
#> 105 chr5 112836165 112836170 TCC
#> 106 chr5 112836165 112836171 TCC
#> 107 chr5 112836180 112836181 G
#> 108 chr5 112838773 112838767 TAAAAC
#> 109 chr5 112838934 112838935 C
#> 110 chr5 112839450 112839451 G
#> 111 chr5 112839474 112839475 C
#> 112 chr5 112839510 112839511 G
#> 113 chr5 112839514 112839508 TAAAAG
#> 114 chr5 112839524 112839525 G
#> 115 chr5 112839527 112839525 TG
#> 116 chr5 112839528 112839529 G
#> 117 chr5 112839558 112839559 G
#> 118 chr5 112839606 112839607 C
#> 119 chr5 112839627 112839628 G
#> 120 chr5 112839651 112839652 G
#> 121 chr5 112839693 112839694 C
#> 122 chr5 112839719 112839716 CTA
#> 123 chr5 112839720 112839718 TA
#> 124 chr5 112839722 112839717 TGTTC
#> 125 chr5 112839726 112839727 C
#> 126 chr5 112839740 112839742 C
#> 127 chr5 112839752 112839743 ATGTACTTC
#> 128 chr5 112839753 112839758 T
#> 129 chr5 112839782 112839779 TGA
#> 130 chr5 112839783 112839784 G
#> 131 chr5 112839787 112839785 GT
#> 132 chr5 112839822 112839810 TGCAGTGGAATG
#> 133 chr5 112839832 112839830 TG
#> 134 chr5 112839835 112839833 TA
#> 135 chr5 112839838 112839836 GT
#> 136 chr5 112839860 112839858 TC
#> 137 chr5 112839871 112839869 GC
#> 138 chr5 112839874 112839875 C
#> 139 chr5 112839875 112839873 TG
#> 140 chr5 112839879 112839880 C
#> 141 chr5 112839890 112839888 AC
#> 142 chr5 112839895 112839892 GCA
#> 143 chr5 112839898 112839892 GAAGTA
#> 144 chr5 112839919 112839917 CT
#> 145 chr5 112839942 112839943 C
#> 146 chr5 112840052 112840054 T
#> 147 chr5 112840054 112840052 CT
#> 148 chr5 112840056 112840053 TTA
#> 149 chr5 112840063 112840065 A
#> 150 chr5 112840072 112840070 CGG
#> 151 chr5 112840072 112840069 CGG
#> 152 chr5 112840078 112840076 GT
#> 153 chr5 112840233 112840296 G
#> 154 chr5 112840254 112840256 G
#> alt DP NV
#> 1 GTT 39 0
#> 2 CTT 1 0
#> 3 G 46 42
#> 4 C 54 52
#> 5 G 34 0
#> 6 T 36 0
#> 7 TTTATTA 36 0
#> 8 ATTT 39 31
#> 9 G 37 0
#> 10 C 38 0
#> 11 G 38 0
#> 12 A 34 0
#> 13 C 34 0
#> 14 G 34 0
#> 15 G 36 0
#> 16 ATT 21 19
#> 17 ATTTT 2 0
#> 18 ATTT 2 0
#> 19 A 2 0
#> 20 GT 43 0
#> 21 T 36 0
#> 22 C 47 38
#> 23 C 42 36
#> 24 G 42 0
#> 25 CTT 37 0
#> 26 C 37 0
#> 27 TAA 0 0
#> 28 TAAA 40 40
#> 29 CAA 5 3
#> 30 A 37 0
#> 31 C 37 0
#> 32 CAA 37 0
#> 33 CTT 40 0
#> 34 CTT 3 0
#> 35 CTTTT 10 7
#> 36 CTTTTT 3 0
#> 37 C 3 0
#> 38 T 39 0
#> 39 AT 6 0
#> 40 ATT 25 19
#> 41 ATTT 6 0
#> 42 CT 37 0
#> 43 T 30 0
#> 44 T 38 0
#> 45 AT 6 2
#> 46 ATT 26 22
#> 47 AGGC 48 42
#> 48 T 36 0
#> 49 A 36 0
#> 50 ATT 36 0
#> 51 C 35 0
#> 52 CAA 37 2
#> 53 CAAAA 35 0
#> 54 T 53 0
#> 55 G 53 0
#> 56 C 29 0
#> 57 CTT 29 0
#> 58 T 22 0
#> 59 G 37 0
#> 60 AT 37 0
#> 61 T 36 0
#> 62 A 34 0
#> 63 A 61 52
#> 64 A 47 0
#> 65 CA 10 10
#> 66 C 37 0
#> 67 G 43 0
#> 68 G 34 0
#> 69 C 34 0
#> 70 G 34 0
#> 71 T 34 0
#> 72 C 35 0
#> 73 CTTTATTTATTTA 36 0
#> 74 C 36 0
#> 75 CTTTA 36 0
#> 76 TG 38 0
#> 77 TAA 39 0
#> 78 T 39 0
#> 79 T 37 0
#> 80 CG 16 10
#> 81 A 38 0
#> 82 A 38 0
#> 83 GAC 36 0
#> 84 G 36 0
#> 85 ATT 43 0
#> 86 A 43 0
#> 87 A 27 2
#> 88 T 28 0
#> 89 TA 36 31
#> 90 T 5 0
#> 91 A 39 0
#> 92 A 40 0
#> 93 AT 32 28
#> 94 A 4 0
#> 95 C 37 0
#> 96 T 28 0
#> 97 TA 16 15
#> 98 T 1 0
#> 99 A 47 41
#> 100 ATT 2 0
#> 101 CTTTTTTTT 0 0
#> 102 CT 0 0
#> 103 TC 13 0
#> 104 T 13 0
#> 105 TTCCCCC 13 0
#> 106 TTCCCCCC 13 0
#> 107 A 5 5
#> 108 T 45 6
#> 109 T 38 0
#> 110 T 37 0
#> 111 T 37 0
#> 112 T 37 0
#> 113 T 37 30
#> 114 T 36 0
#> 115 T 36 0
#> 116 T 36 0
#> 117 T 36 0
#> 118 T 36 0
#> 119 T 36 0
#> 120 T 36 0
#> 121 T 37 0
#> 122 C 37 0
#> 123 T 37 0
#> 124 T 37 0
#> 125 T 37 0
#> 126 CA 37 0
#> 127 A 37 0
#> 128 TGTAC 37 0
#> 129 T 37 0
#> 130 T 37 0
#> 131 G 37 0
#> 132 T 37 0
#> 133 T 37 0
#> 134 T 37 0
#> 135 G 37 0
#> 136 T 37 0
#> 137 G 37 0
#> 138 T 37 0
#> 139 T 37 0
#> 140 T 37 0
#> 141 A 37 0
#> 142 G 37 0
#> 143 G 37 0
#> 144 C 37 0
#> 145 T 37 0
#> 146 TA 36 0
#> 147 C 36 0
#> 148 T 36 0
#> 149 AT 36 0
#> 150 CG 36 0
#> 151 C 36 0
#> 152 G 37 0
#> 153 GCTGGCATCTGGATTTCAGACTTCTGGCTTCCAGAACTGTGGAAGAAGACATCTCGTTGTTTT 35 0
#> 154 GA 35 0
#> VAF Samples
#> 1 0.00000000 A002C204
#> 2 0.00000000 A002C204
#> 3 0.91304348 A002C204
#> 4 0.96296296 A002C204
#> 5 0.00000000 A002C204
#> 6 0.00000000 A002C204
#> 7 0.00000000 A002C204
#> 8 0.79487179 A002C204
#> 9 0.00000000 A002C204
#> 10 0.00000000 A002C204
#> 11 0.00000000 A002C204
#> 12 0.00000000 A002C204
#> 13 0.00000000 A002C204
#> 14 0.00000000 A002C204
#> 15 0.00000000 A002C204
#> 16 0.90476190 A002C204
#> 17 0.00000000 A002C204
#> 18 0.00000000 A002C204
#> 19 0.00000000 A002C204
#> 20 0.00000000 A002C204
#> 21 0.00000000 A002C204
#> 22 0.80851064 A002C204
#> 23 0.85714286 A002C204
#> 24 0.00000000 A002C204
#> 25 0.00000000 A002C204
#> 26 0.00000000 A002C204
#> 27 0.00000000 A002C204
#> 28 1.00000000 A002C204
#> 29 0.60000000 A002C204
#> 30 0.00000000 A002C204
#> 31 0.00000000 A002C204
#> 32 0.00000000 A002C204
#> 33 0.00000000 A002C204
#> 34 0.00000000 A002C204
#> 35 0.70000000 A002C204
#> 36 0.00000000 A002C204
#> 37 0.00000000 A002C204
#> 38 0.00000000 A002C204
#> 39 0.00000000 A002C204
#> 40 0.76000000 A002C204
#> 41 0.00000000 A002C204
#> 42 0.00000000 A002C204
#> 43 0.00000000 A002C204
#> 44 0.00000000 A002C204
#> 45 0.33333333 A002C204
#> 46 0.84615385 A002C204
#> 47 0.87500000 A002C204
#> 48 0.00000000 A002C204
#> 49 0.00000000 A002C204
#> 50 0.00000000 A002C204
#> 51 0.00000000 A002C204
#> 52 0.05405405 A002C204
#> 53 0.00000000 A002C204
#> 54 0.00000000 A002C204
#> 55 0.00000000 A002C204
#> 56 0.00000000 A002C204
#> 57 0.00000000 A002C204
#> 58 0.00000000 A002C204
#> 59 0.00000000 A002C204
#> 60 0.00000000 A002C204
#> 61 0.00000000 A002C204
#> 62 0.00000000 A002C204
#> 63 0.85245902 A002C204
#> 64 0.00000000 A002C204
#> 65 1.00000000 A002C204
#> 66 0.00000000 A002C204
#> 67 0.00000000 A002C204
#> 68 0.00000000 A002C204
#> 69 0.00000000 A002C204
#> 70 0.00000000 A002C204
#> 71 0.00000000 A002C204
#> 72 0.00000000 A002C204
#> 73 0.00000000 A002C204
#> 74 0.00000000 A002C204
#> 75 0.00000000 A002C204
#> 76 0.00000000 A002C204
#> 77 0.00000000 A002C204
#> 78 0.00000000 A002C204
#> 79 0.00000000 A002C204
#> 80 0.62500000 A002C204
#> 81 0.00000000 A002C204
#> 82 0.00000000 A002C204
#> 83 0.00000000 A002C204
#> 84 0.00000000 A002C204
#> 85 0.00000000 A002C204
#> 86 0.00000000 A002C204
#> 87 0.07407407 A002C204
#> 88 0.00000000 A002C204
#> 89 0.86111111 A002C204
#> 90 0.00000000 A002C204
#> 91 0.00000000 A002C204
#> 92 0.00000000 A002C204
#> 93 0.87500000 A002C204
#> 94 0.00000000 A002C204
#> 95 0.00000000 A002C204
#> 96 0.00000000 A002C204
#> 97 0.93750000 A002C204
#> 98 0.00000000 A002C204
#> 99 0.87234043 A002C204
#> 100 0.00000000 A002C204
#> 101 0.00000000 A002C204
#> 102 0.00000000 A002C204
#> 103 0.00000000 A002C204
#> 104 0.00000000 A002C204
#> 105 0.00000000 A002C204
#> 106 0.00000000 A002C204
#> 107 1.00000000 A002C204
#> 108 0.13333333 A002C204
#> 109 0.00000000 A002C204
#> 110 0.00000000 A002C204
#> 111 0.00000000 A002C204
#> 112 0.00000000 A002C204
#> 113 0.81081081 A002C204
#> 114 0.00000000 A002C204
#> 115 0.00000000 A002C204
#> 116 0.00000000 A002C204
#> 117 0.00000000 A002C204
#> 118 0.00000000 A002C204
#> 119 0.00000000 A002C204
#> 120 0.00000000 A002C204
#> 121 0.00000000 A002C204
#> 122 0.00000000 A002C204
#> 123 0.00000000 A002C204
#> 124 0.00000000 A002C204
#> 125 0.00000000 A002C204
#> 126 0.00000000 A002C204
#> 127 0.00000000 A002C204
#> 128 0.00000000 A002C204
#> 129 0.00000000 A002C204
#> 130 0.00000000 A002C204
#> 131 0.00000000 A002C204
#> 132 0.00000000 A002C204
#> 133 0.00000000 A002C204
#> 134 0.00000000 A002C204
#> 135 0.00000000 A002C204
#> 136 0.00000000 A002C204
#> 137 0.00000000 A002C204
#> 138 0.00000000 A002C204
#> 139 0.00000000 A002C204
#> 140 0.00000000 A002C204
#> 141 0.00000000 A002C204
#> 142 0.00000000 A002C204
#> 143 0.00000000 A002C204
#> 144 0.00000000 A002C204
#> 145 0.00000000 A002C204
#> 146 0.00000000 A002C204
#> 147 0.00000000 A002C204
#> 148 0.00000000 A002C204
#> 149 0.00000000 A002C204
#> 150 0.00000000 A002C204
#> 151 0.00000000 A002C204
#> 152 0.00000000 A002C204
#> 153 0.00000000 A002C204
#> 154 0.00000000 A002C204
data.frame(cna)
#> chr from to Major minor Samples
#> 1 1 822668 1985814 1 1 A002C204
#> 2 1 1985815 2008141 2 2 A002C204
#> 3 1 2008142 13911153 1 1 A002C204
#> 4 1 13911154 13959414 3 0 A002C204
#> 5 1 13959415 121764540 1 1 A002C204
#> 6 1 121764541 121782089 2 0 A002C204
#> 7 1 121782090 122632098 2 1 A002C204
#> 8 1 122632099 122684264 2 0 A002C204
#> 9 1 122684265 123395250 2 1 A002C204
#> 10 1 123395251 123409594 4 0 A002C204
#> 11 1 123409595 123764103 2 1 A002C204
#> 12 1 123764104 124909534 3 1 A002C204
#> 13 1 124909535 125073299 1 1 A002C204
#> 14 1 125073300 125115406 2 0 A002C204
#> 15 1 125115407 134442991 2 1 A002C204
#> 16 1 134442992 153687686 1 1 A002C204
#> 17 1 153687687 153725910 2 1 A002C204
#> 18 1 153725911 160695304 1 1 A002C204
#> 19 1 160695305 160697028 2 0 A002C204
#> 20 1 160697029 234775059 1 1 A002C204
#> 21 1 234775060 234782142 3 1 A002C204
#> 22 1 234782143 248903660 1 1 A002C204
#> 23 2 10797 89353653 1 1 A002C204
#> 24 2 89353654 89958704 2 1 A002C204
#> 25 2 89958705 90807134 1 1 A002C204
#> 26 2 90807135 94158750 2 1 A002C204
#> 27 2 94158751 240879852 1 1 A002C204
#> 28 2 240879853 240883002 2 2 A002C204
#> 29 2 240883003 242058566 1 1 A002C204
#> 30 3 57400 90748398 1 1 A002C204
#> 31 3 90748399 93254302 2 1 A002C204
#> 32 3 93254303 190199629 1 1 A002C204
#> 33 3 190199630 190202394 5 3 A002C204
#> 34 3 190202395 195697804 1 1 A002C204
#> 35 3 195697805 195711892 2 1 A002C204
#> 36 3 195711893 198113136 1 1 A002C204
#> 37 4 85866 42771923 1 1 A002C204
#> 38 4 42771924 42773322 2 0 A002C204
#> 39 4 42773323 49360128 1 1 A002C204
#> 40 4 49360129 49640652 4 0 A002C204
#> 41 4 49640653 50512170 2 1 A002C204
#> 42 4 50512171 188504076 1 1 A002C204
#> 43 4 188504077 188507054 1 0 A002C204
#> 44 4 188507055 189872692 1 1 A002C204
#> 45 5 12041 46512789 2 0 A002C204
#> 46 5 46512790 50148080 2 1 A002C204
#> 47 5 50148081 159916549 2 0 A002C204
#> 48 5 159916550 159924351 1 1 A002C204
#> 49 5 159924352 175911088 2 0 A002C204
#> 50 5 175911089 176032464 1 1 A002C204
#> 51 5 176032465 181271629 2 0 A002C204
#> 52 6 171649 250034 1 1 A002C204
#> 53 6 250035 382392 2 1 A002C204
#> 54 6 382393 35781648 1 1 A002C204
#> 55 6 35781649 35799023 2 1 A002C204
#> 56 6 35799024 60232108 1 1 A002C204
#> 57 6 60232109 60235249 2 0 A002C204
#> 58 6 60235250 155026833 1 1 A002C204
#> 59 6 155026834 155029916 4 4 A002C204
#> 60 6 155029917 170597327 1 1 A002C204
#> 61 7 41888 62342668 2 1 A002C204
#> 62 7 62342669 62343413 2 0 A002C204
#> 63 7 62343414 81358228 2 1 A002C204
#> 64 7 81358229 81359971 2 0 A002C204
#> 65 7 81359972 100952610 2 1 A002C204
#> 66 7 100952611 100961172 3 1 A002C204
#> 67 7 100961173 144779724 2 1 A002C204
#> 68 7 144779725 144781900 4 4 A002C204
#> 69 7 144781901 159329969 2 1 A002C204
#> 70 8 220692 6957548 1 1 A002C204
#> 71 8 6957549 8646974 2 1 A002C204
#> 72 8 8646975 8824464 1 1 A002C204
#> 73 8 8824465 8948930 2 1 A002C204
#> 74 8 8948931 9069558 1 1 A002C204
#> 75 8 9069559 9243576 2 1 A002C204
#> 76 8 9243577 9370558 1 1 A002C204
#> 77 8 9370559 9456231 2 1 A002C204
#> 78 8 9456232 13032581 1 1 A002C204
#> 79 8 13032582 13053099 2 1 A002C204
#> 80 8 13053100 21760352 1 1 A002C204
#> 81 8 21760353 22099509 2 1 A002C204
#> 82 8 22099510 22725141 1 1 A002C204
#> 83 8 22725142 22990366 2 1 A002C204
#> 84 8 22990367 25038967 1 1 A002C204
#> 85 8 25038968 25158108 2 1 A002C204
#> 86 8 25158109 25927974 1 1 A002C204
#> 87 8 25927975 26226254 2 1 A002C204
#> 88 8 26226255 37523720 1 1 A002C204
#> 89 8 37523721 38597754 2 1 A002C204
#> 90 8 38597755 39994712 1 1 A002C204
#> 91 8 39994713 40269844 2 1 A002C204
#> 92 8 40269845 41334544 1 1 A002C204
#> 93 8 41334545 41476523 2 1 A002C204
#> 94 8 41476524 42102888 1 1 A002C204
#> 95 8 42102889 42783768 2 1 A002C204
#> 96 8 42783769 69844424 1 1 A002C204
#> 97 8 69844425 70021513 2 1 A002C204
#> 98 8 70021514 72181818 1 1 A002C204
#> 99 8 72181819 72183076 4 2 A002C204
#> 100 8 72183077 80155517 1 1 A002C204
#> 101 8 80155518 80592485 2 1 A002C204
#> 102 8 80592486 94620405 1 1 A002C204
#> 103 8 94620406 94966532 2 1 A002C204
#> 104 8 94966533 97433968 1 1 A002C204
#> 105 8 97433969 97819902 2 1 A002C204
#> 106 8 97819903 102421227 1 1 A002C204
#> 107 8 102421228 102715420 2 1 A002C204
#> 108 8 102715421 119841344 1 1 A002C204
#> 109 8 119841345 120159806 2 1 A002C204
#> 110 8 120159807 125243048 1 1 A002C204
#> 111 8 125243049 125481604 2 1 A002C204
#> 112 8 125481605 127589052 1 1 A002C204
#> 113 8 127589053 127828578 2 1 A002C204
#> 114 8 127828579 133533319 1 1 A002C204
#> 115 8 133533320 133704132 2 1 A002C204
#> 116 8 133704133 139996605 1 1 A002C204
#> 117 8 139996606 142188974 2 1 A002C204
#> 118 8 142188975 142379368 1 1 A002C204
#> 119 8 142379369 142657086 2 1 A002C204
#> 120 8 142657087 142837858 1 1 A002C204
#> 121 8 142837859 143521131 2 1 A002C204
#> 122 8 143521132 143617574 1 1 A002C204
#> 123 8 143617575 144962821 2 1 A002C204
#> 124 8 144962822 145071631 1 1 A002C204
#> 125 9 204014 39180130 1 1 A002C204
#> 126 9 39180131 40912086 2 1 A002C204
#> 127 9 40912087 40915793 2 0 A002C204
#> 128 9 40915794 62869874 2 1 A002C204
#> 129 9 62869875 129404868 1 1 A002C204
#> 130 9 129404869 129485292 2 1 A002C204
#> 131 9 129485293 138124865 1 1 A002C204
#> 132 10 91366 38242652 1 1 A002C204
#> 133 10 38242653 38522852 2 1 A002C204
#> 134 10 38522853 38690962 1 1 A002C204
#> 135 10 38690963 38813996 2 1 A002C204
#> 136 10 38813997 38816054 2 0 A002C204
#> 137 10 38816055 38941858 2 1 A002C204
#> 138 10 38941859 39571988 1 1 A002C204
#> 139 10 39571989 41522648 2 1 A002C204
#> 140 10 41522649 41530557 2 0 A002C204
#> 141 10 41530558 41649224 2 1 A002C204
#> 142 10 41649225 42231738 1 1 A002C204
#> 143 10 42231739 42303078 2 0 A002C204
#> 144 10 42303079 46522963 1 1 A002C204
#> 145 10 46522964 46541968 2 1 A002C204
#> 146 10 46541969 108547330 1 1 A002C204
#> 147 10 108547331 108549138 5 3 A002C204
#> 148 10 108549139 133622305 1 1 A002C204
#> 149 11 196944 51155272 1 1 A002C204
#> 150 11 51155273 54545390 2 1 A002C204
#> 151 11 54545391 135075590 1 1 A002C204
#> 152 12 21064 38052 1 1 A002C204
#> 153 12 38053 70274 2 1 A002C204
#> 154 12 70275 34801010 1 1 A002C204
#> 155 12 34801011 37262642 2 1 A002C204
#> 156 12 37262643 133240522 1 1 A002C204
#> 157 13 16003441 38955993 2 1 A002C204
#> 158 13 38955994 38956733 6 2 A002C204
#> 159 13 38956734 114328229 2 1 A002C204
#> 160 14 16097169 16109122 1 0 A002C204
#> 161 14 16109123 16137230 2 1 A002C204
#> 162 14 16137231 17181838 3 1 A002C204
#> 163 14 17181839 106874228 1 1 A002C204
#> 164 15 17009590 17021518 1 1 A002C204
#> 165 15 17021519 17030497 3 0 A002C204
#> 166 15 17030498 22024845 2 1 A002C204
#> 167 15 22024846 57762495 1 1 A002C204
#> 168 15 57762496 57763216 3 0 A002C204
#> 169 15 57763217 101633478 1 1 A002C204
#> 170 16 46987 16414866 1 1 A002C204
#> 171 16 16414867 16700565 2 1 A002C204
#> 172 16 16700566 22504980 1 1 A002C204
#> 173 16 22504981 22699922 2 1 A002C204
#> 174 16 22699923 36277740 1 1 A002C204
#> 175 16 36277741 46428446 2 1 A002C204
#> 176 16 46428447 70046418 1 1 A002C204
#> 177 16 70046419 70229015 2 1 A002C204
#> 178 16 70229016 90051298 1 1 A002C204
#> 179 17 143015 12650427 1 1 A002C204
#> 180 17 12650428 12653101 4 4 A002C204
#> 181 17 12653102 21751028 1 1 A002C204
#> 182 17 21751029 21855518 2 1 A002C204
#> 183 17 21855519 21858186 2 0 A002C204
#> 184 17 21858187 22726028 1 1 A002C204
#> 185 17 22726029 26769088 2 1 A002C204
#> 186 17 26769089 26836150 2 0 A002C204
#> 187 17 26836151 83204151 1 1 A002C204
#> 188 18 132671 15195206 1 1 A002C204
#> 189 18 15195207 20874209 2 1 A002C204
#> 190 18 20874210 61969008 1 1 A002C204
#> 191 18 61969009 61971189 4 3 A002C204
#> 192 18 61971190 80248182 1 1 A002C204
#> 193 19 263280 1524112 2 1 A002C204
#> 194 19 1524113 1775290 3 2 A002C204
#> 195 19 1775291 8097458 2 1 A002C204
#> 196 19 8097459 8268512 3 2 A002C204
#> 197 19 8268513 24369446 2 1 A002C204
#> 198 19 24369447 24896730 3 1 A002C204
#> 199 19 24896731 24897864 3 0 A002C204
#> 200 19 24897865 27242278 3 1 A002C204
#> 201 19 27242279 27354712 2 1 A002C204
#> 202 19 27354713 27407438 3 1 A002C204
#> 203 19 27407439 58580561 2 1 A002C204
#> 204 20 61083 26331013 1 1 A002C204
#> 205 20 26331014 26345356 2 0 A002C204
#> 206 20 26345357 28784970 2 1 A002C204
#> 207 20 28784971 28826332 2 0 A002C204
#> 208 20 28826333 28886948 2 1 A002C204
#> 209 20 28886949 28904928 2 0 A002C204
#> 210 20 28904929 30064009 2 1 A002C204
#> 211 20 30064010 64281506 1 1 A002C204
#> 212 21 7324287 7325448 2 1 A002C204
#> 213 21 7325449 7325732 2 0 A002C204
#> 214 21 7325733 7326344 2 1 A002C204
#> 215 21 7326345 7919116 2 0 A002C204
#> 216 21 7919117 7925434 3 1 A002C204
#> 217 21 7925435 7954084 2 0 A002C204
#> 218 21 7954085 10701814 3 1 A002C204
#> 219 21 10701815 10702238 2 0 A002C204
#> 220 21 10702239 10705696 2 1 A002C204
#> 221 21 10705697 10705967 2 0 A002C204
#> 222 21 10705968 10758066 3 1 A002C204
#> 223 21 10758067 10758828 2 0 A002C204
#> 224 21 10758829 10784464 2 1 A002C204
#> 225 21 10784465 11889812 3 1 A002C204
#> 226 21 11889813 13493784 2 1 A002C204
#> 227 21 13493785 46672164 1 1 A002C204
#> 228 22 11219527 12401808 2 1 A002C204
#> 229 22 12401809 12402615 2 0 A002C204
#> 230 22 12402616 12423085 2 1 A002C204
#> 231 22 12423086 22584056 1 1 A002C204
#> 232 22 22584057 22587092 2 2 A002C204
#> 233 22 22587093 40151354 1 1 A002C204
#> 234 22 40151355 40171254 2 2 A002C204
#> 235 22 40171255 44414652 1 1 A002C204
#> 236 22 44414653 44449100 2 1 A002C204
#> 237 22 44449101 50736234 1 1 A002C204
data.frame(purity)
#> Purity
#> 1 0.805
x = init(snvs,
cna,
purity,
ref = "hg38")
#> [ CNAqc - CNA Quality Check ]
#> ℹ Using reference genome coordinates for: hg38.
#> Warning in fortify_mutation_calls(snvs): You are using indels mutation data,
#> just beware that indels count-values aree less reliable than SNVs ones ....
#> ! Missing CCF column from CNA calls, adding CCF = 1 assuming clonal CNA calls.
#> ! Missing segments length from CNA calls, adding it to CNA calls.
#> ! CNA chromosomes should be in the format 'chr*', I will add a 'chr' prefix.
#> ℹ Input n = 154 mutations for 237 CNA segments (237 clonal, 0 subclonal)
#> ✓ Mapped n = 154 mutations to clonal segments (100% of input)
snvs.samp = x$snvs
cna.samp = x$cna
pure.samp = x$purity
ccf = compute_CCF(x)
#> ── Computing mutation multiplicity for karyotype 2:0 using the entropy method. ─
#> ℹ Expected Binomial peak(s) for these calls (1 and 2 copies):
#> Error in dbinom(NV, size = n, prob = p): Non-numeric argument to mathematical function
ccf.data = CCF(ccf)
#> Error in CCF(ccf): inherits(x, "cnaqc") is not TRUE
ccf.data$CCF[ccf.data$CCF>=1] = 1
#> Error in ccf.data$CCF[ccf.data$CCF >= 1] = 1: object 'ccf.data' not found
ccfs[[sample]] = ccf.data
#> Error in eval(expr, envir, enclos): object 'ccf.data' not found
Created on 2020-11-17 by the reprex package (v0.3.0.9001)
Thank you very much. Please let me know if you need any more details.
The reprex is clear, thanks, and I should be able to fix it -- maybe is the fact that some mutations have 0 DP and 0 VAF and you get some NA somewhere? Btw, could you link here file "~/Desktop/cnaquestion.RData"
so I can avoid copy-pasting from this shell and parsing the input?
Sending it to gcaravagn@gmail.com would work too - thanks.
Though this shows up as a comment…this is an email to the email yoou posted below too with that linked file
Thank you!
On Nov 17, 2020, at 2:29 PM, Giulio Caravagna notifications@github.com wrote:
Sending it to gcaravagn@gmail.com mailto:gcaravagn@gmail.com would work too - thanks.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/caravagn/CNAqc/issues/4#issuecomment-729252682, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY3HY77S4WRUD7COBRGHI3SQL2OBANCNFSM4TQAQ5IQ.
From whaat I could tell it had to do with the Karyotype being 2:0 for this set of mutations. In this dataset, all the mutations are from a single gene which are from a single segment which inn this case is 2:0.
But of course I’ll defer to your expertise on the software. Thats just what I could determine from my little investigation.
I look forward to seeing what the issue was.
I may have another issue in the future too but one thing at a time :)
On Nov 17, 2020, at 2:29 PM, Giulio Caravagna notifications@github.com wrote:
The reprex is clear, thanks, and I should be able to fix it -- maybe is the fact that some mutations have 0 DP and 0 VAF and you get some NA somewhere? Btw, could you link here file "~/Desktop/cnaquestion.RData" so I can avoid copy-pasting from this shell and parsing the input?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/caravagn/CNAqc/issues/4#issuecomment-729252363, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABY3HY7G7MOSSVQRX26NI7DSQL2LHANCNFSM4TQAQ5IQ.
Hey, I've fixed it. There was a problem for a weird case I did not consider. Now it works and computes CCF for your data. Thanks (PS I did improve some other visualisations etc.)
See [4a1d37f]
Im very excited to use this software, thank you so much for preparing it.
I've run into an issue with a finicky sample can I can't figure out what's wrong.
However I get an error for only one of my samples at this function...
its worth noting that all the samples before this one had a Karyotype of 1:1 but this sample had 2:0.
Any suggestions?
Thank you!