Closed selkamand closed 3 months ago
@selkamand Hi, thank you for bringing this to my attention. Due to the removal of the copynumber package from Bioc, I had to remove it from the dependencies in v2.2.0 (News). You can install the package from https://github.com/shixiangwang/copynumber. It is generally recommended as I have added some features, although other forks of this package exist on GitHub. I will update the readme to include instructions on how to install the copynumber package.
I had considered directly copying the code of pcf
to sigminer; however, the deep dependencies were hard to handle, so I gave up on that approach. This is why I used pcf = "copynumber"%:::%"pcf"
to import the function and avoid CRAN check at the same time.
Thanks @ShixiangWang
Thanks for your work on this package!
Just noticed that SV getDists function has a couple of issues
copynumber
package that is not declared in package documentation / DESCRIPTION fileWould it be possible to