Should I plot with methylDiff or methylBase object?
Hi,
I have been processing RBBS data with methylKit following the vignette. I now have a methylDiff object, a methylBase object, and also a percentage matrix. Let's say I want to plot a specific region in chromosome 11 at a specific gene using rtracklayer to see if there is hypomethylation in my treatment group. Should I use the methylDiff object as input into GRanges or the methylBase object?
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