The PureCN overview manual recommends providing a COSMIC VCF to PureCN with the --cosmic.vcf.file option to runAbsoluteCN() or to add a Cosmic.CNT INFO field to the VCF. I am using PureCN.R to run runAbsoluteCN(), but I don't see an argument for it that will allow me to provide the COSMIC VCF. It makes me wonder again if I should move away from using PureCN.R and just call the functions directly?

What would be nice is to have some way to automatically be able to know what option to give PureCN.R for any given runAbsoluteCN() argument (or any other function called by PureCN.R). Maybe something like:

RScript PureCN.R .....    --runAbsoluteCN --cosmic.vcf.file COSMIC.vcf.gz

Another question: COSMIC VCF files are divided into a coding mutation vcf and a noncoding variant vcf. Is it correct to assume that PureCN wants only the former?

Looks like this option is indeed missing in PureCN.R. Our pipelines add the Cosmic annotation upstream, so I don't use that function, but should work (albeit slow I guess with the current huge Cosmic VCFs - you can speed it up by pre-filtering the VCF for a minimum CNT info field). All PureCN does is to adjust the somatic prior of variants with the specified minimum Cosmic count.

I'll add it to PureCN.R in the next version. You probably don't want to update only for this, but you can manually add the argument in PureCN.R when it calls runAbsoluteCN. So make a copy of PureCN.R and add it there for now. Sorry I don't have a better solution.

I try to at least keep a mapping of the command line arguments and corresponding R package function arguments in the Appendix of https://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html