Gavin Ha

The `--alphaK` assigns a pseudocount (e.g. 10000) to each of the states. Since there are 11 states, then each of the 11 states will be set to 10000. `--alphaKHigh` is...

@fpbarthel The copy number segments are usually nice to look at but it is more difficult to assess the solutions. The plots that I like to use are the `CNA.pdf`...

Hi @Kcjohnson and @fpbarthel Thanks for sharing your experiences with TITAN and bringing up the concern regarding ploidy. Frankly, selecting the correct ploidy solution is a very challenging problem that...

Hi @fpbarthel For cancer cell fraction estimates of SNVs, I recommend you check out PyClone and PhyloWGS (and other similar tools). Their corresponding papers will have descriptions of how they...

Hi @sengoku93 There are many reasons for this error. Usually, errors that occur during parameter estimation are related to - very noisy data - incorrect input data Is this error...

Hi @MUppal Thanks for bringing this up and pointing out where the problem is. I forgot to run my unit test cases for targeted capture analysis. Hopefully this patch fixes...

Hi @haoziyeung Can you provide the `sessionInfo()` so that we can see the version of R and other packages? Thanks, Gavin

Hi @haoziyeung We have never encountered this error. This is what I could find searching this error on Google. https://support.bioconductor.org/p/93695/ It might have something to do with R versions and...

Hi @Isy89 I made a quick change to GRanges. Please give it a try and let me know if there are any problems. I will leave this issue open until...

Hi @cebercoto I have tried to address all the RangedData deprecation issues and it runs fine for me. If you found another problem, please do show me the output of...