ENmix: how to combine oxBS.MLE with RCP?
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joannew • 0
Last seen 1 day ago

I've been testing out the preprocessing functions in ENmix on my EPIC array data, which includes bisulfite and oxidative bisulfite treated samples. I've run preprocessENmix then norm.quantile then rcp. I would like to now run oxBS.MLE, but rcp outputs just the beta matrix, not a methylset, so I don't have the sum(meth+unmeth) matrix needed for MLE. Is there a way around this? The rcp probe bias correction seems to greatly improve the beta distributions of my oxBS data, so I would like to include that step. Is there a way to output a methylset from the rcp function? Or a way to regenerate the meth & unmeth signals? Or an alternate probe bias correction function that might work here? Many thanks for suggestions!

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