Hello,
We currently don’t have a specific threshold recommendation, but perhaps the discussion in this thread could be helpful.
And in case you are interested in absolute copy number calls instead of relative to classify CNAs, we currently have data generated by the ABSOLUTE algorithm on the CCLE lines. You can find the file called CCLE_ABSOLUTE_combined_20181227 in the “CCLE 2019” data set on the download page. We are also working on running PureCN on all of our current DepMap data for absolute copy number calls, and we’re hoping to include it as part of the release in the future.
Hope this helps!
Simone
