Hello,

I have been using exomeCopy with no problem; however I was wondering if anyone has any insight about setting the possible copy number while running the exomeCopy function to get CNVs? I have trid both S=1:4 or 1:6 but I'm not sure if there is a general rule for this. Can I set 1:4 only? Do I need to use 1:6? Or is 1:10 even?

Basically it's the S setting in the following sample code:

fit <- exomeCopy(example.counts["chr1"], sample.name = exome.samples[3], X.names = c("log.bg", "GC", "GC.sq", "width"), S = 0:6, + d = 2)

Any suggestion is appreciated. Thanks!

I would recommend staying within 0:6 (where 2 is normal diploid, so allowing for triplication). Or if you need to go higher, because you suspect there are more than triplication in the samples, I'd recommend you switch to something like ExomeCNV, which allows arbitrary values in its use of the DNAcopy CBS algorithm.