ahorn720
commented
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 copiesso maybe it needs to have the column names renamed or something like that.
luca-dex
caravagn
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!