min.per.group and cov.bases

[Kristina Santucci]

Hi,

I was hoping to get some clarification on the min.per.group and cov.bases parameters (for a CpG only analysis). Lets say I have 4 controls and 4 treatments and I unite this with a min.per.group = 3, from my understanding CpG bases must be covered in 3/4 samples for both groups. Then when I tile regions of 200bp and set cov.bases = 2, does this mean at least 2 CpG bases must be present in the region for DMR calling (both having coverage in 3/4 samples as filtered earlier), OR do CpG sites in that 200 bp region must only be covered by two samples from either group to be considered for DMR calling? In either case, on what grounds would a 200bp region be discarded?

Thank you in advance for the clarification.