Markus Riester

I just added a function adjustLogRatio() to the issue_40 branch. It has an argument is.log2 that's by default TRUE. Let me how it goes and I'll add it to the...

I use -8 as minimum log2 ratio in other parts. If that causes problems, let me know. Basically -8 is the smallest possible log ratio in a 99% purity sample.

Will change the default to 2^-8. 0.004 is indeed a bit confusing.

Hi @akaviaLab . never seen this one before. You are using a slightly older version. Don't think it's fixed, but you can easily update with: BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18") Does...

Yes, it looks like the Inf values causing issues are generated somehow by the PSCBS segmentation. I would need debug data to dig deeper. Let me know if you can...

You can also try turning off off-target reads. They don't help much with WES. There is a parameter to specify the minimum fraction of intervals being off-target. If that fixes...

Anything higher than what you have works. 228926 on-target, 16245 off-target, so even 0.1 would do. yes, GATK should still be fine.

That's a valid feature request. I'll see when I have time for this. If urgent, you probably for now are faster correcting the interval file gene column manually.

Hi @ShvartsmanIrina, I never had a chance to look into this. See #159. It would need some benchmarking. Any help appreciated. See also https://ascopubs.org/doi/10.1200/GO.2023.9.Supplement_1.89 https://www.mdpi.com/2072-6694/15/13/3445.

Apologies, was out of office and will get back to you soon.