How should I compare multiple TF methylation percentages?

Question

[morovatunc]

Hi,

I would like to compare methylation percentage of multiple transcription factors. I have seen many differential methylation region analysis based on multiple samples but has any of you done this kind of analysis based on single sample and different subset of regions ?

My aim is to score every region of a bed file regarding its methylation percentage. So that I can get cumulative scores of that TF and make comparison.

• For any given peak of a bed file how should I score methylation ?
• Because methylation data is bimodal a simple box plot is looking very bad. Do you have a suggestion to show differences among TF binding regions methylation profile ?

I am very frasturated so any guidenence is very valuable,

Best,

Tunc.