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, X.names = c("log.bg", "GC", "GC.sq", "width"), S = 0:6, + d = 2)
Any suggestion is appreciated. Thanks!