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?