I have a set of BS and oxBS treated samples from EPICarray and would like to analyze them using a R package. I found there are oxyBS and oxBS-MLE packages but I am struggling with their implementation to the analysis itself. For the methylation analysis I use the ChAMP and minfi packages so can anyone give me a hint how to combine those with any of the oxBS analyzing methods?
Or does anyone have a suggestion of any other analyzing method for assessing hydroxymethylation differences?
Thanks in advance!!