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caravagnalab / CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package
GNU General Public License v3.0
14 stars 8 forks source link

Request to fix 2 bugs #37

Closed Kazuki526 closed 1 week ago

Kazuki526 commented 1 month ago

Hi, thank you for great tools. I found two bugs, so please fix them.

  1. An error occurs when supported_peaks = c(“1:0”, “1:1”, “2:0”, “2:1”, “2:2”) is not present in the karyotype of subclonal CNA.

  2. In the function called single_run() within simple_peak_detector(), it occasionally throws an error saying 'Assigned data hst[round(pks$x * 100)] must be compatible with existing data.'. I think that this is probably an error that occurs when peak_algorithms.R line 735 'round(pks$x * 100)' contains a zero. Therefore, I think that changing line 730 dplyr::filter(x <= 1, x >= 0) to dplyr::filter(x <= 1, x >0) will solve the problem.

caravagn commented 1 month ago

hi, if you can show an example input data for both cases we can fix your stuff

AliceAntonello commented 1 month ago

Can you also post an example of the code you are using?

caravagn commented 2 weeks ago

Cannot reproduce.

Kazuki526 commented 2 weeks ago

Sorry for the delay. I will upload example data and scripts for errors 1 and 2. My apologies. For error 2 I may have made a mistake in what I thought was the cause of the error. exdata.zip

caravagn commented 1 week ago

OK we are re-opening and will look into your data (@AliceAntonello )

AliceAntonello commented 1 week ago

The two bugs are fixed now, let us know if everything works

Kazuki526 commented 1 week ago

Thank you very much for your quick help!