for the mode "ID", error

eajeong commented 9 months ago

Hello, I have a question about the error message as follows.

I used maf files from TCGAmutations. For the mode "ID", I got an error as "More than 2 regions counted, please report your data and code to developer!"

Euna

brca <- tcga_load("BRCA")
mt_tally_ID <- sig_tally(
  brca,
  ref_genome = "BSgenome.Hsapiens.UCSC.hg19",
  use_syn = TRUE,
  mode = "ID",
  add_trans_bias = TRUE
)

ℹ [2023-12-05 14:33:32.010136]: INDEL matrix generation - start. ✔ [2023-12-05 14:33:34.646027]: Reference sequences queried from genome. ✔ [2023-12-05 14:33:34.669403]: INDEL length extracted. ✔ [2023-12-05 14:33:34.92571]: Adjacent copies counted. ✔ [2023-12-05 14:37:07.416215]: Microhomology size calculated. ✔ [2023-12-05 14:37:07.795835]: INDEL records classified into different components (types). ✔ [2023-12-05 14:37:07.821577]: ID-28 matrix created. ✔ [2023-12-05 14:37:07.847312]: ID-83 matrix created. ✖ [2023-12-05 14:37:07.973748]: More than 2 regions counted, please report your data and code to developer!

ShixiangWang commented 9 months ago

Hi @eajeong , thanks for reporting. It's a bug related to counting when trans bias is enabled.

Please update sigminer by BiocManager::install("shixiangwang/sigminer") and try again.

eajeong commented 9 months ago

Thank you for your help.

ShixiangWang / sigminer

for the mode "ID", error #445