can anybody give some advice on how to compute Fst values between populations given a set of epigenetic modifications associated to those populations. Let say I have the information on what is methylated in my genome in 4 populations (2 controls and 2 exposed to something that causes epigenetic changes - at least this is my hypothesis) How would I compute whether my control populations differ from my modified populations ? Fst? Lets just focus on methylations because once I understand the principle on how to compute Fst on this data I'll know how to apply it to other data sets. (In case of methylations do i need to first determine the differences using for example methylKit??) How to start?
What I have : I have mapped reads associated to methylated regions in my genome
Any advice ???