Is there a way to export the smoothed methylation values from DMRseq across the entire genome? I'd like to store them in bigWig file to view in a genome browser.
Hi swebb1,
dmrseq does not compute smoothed methylation values. Instead, it smooths methylation differences with respect to the covariate of interest. These smoothed methylation differences are not stored. If obtaining these values would be useful, I would consider adding an option to store/export them. If you are interested in obtaining smoothed methylation values, you can obtain these via the BSmooth() function in the bsseq package.
Best,
Keegan
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version 2.3.6
Hi Keegan,
I was essentially looking for the lines plotted in plotDMRs() function but I assume these are just created on the fly. I will run BSmooth for the entire genome for now, thanks for your help.
Ah, yes the smoothed lines generated in plotDMRs() for visualization purposes are generated on the fly, so they are not created for the entire genome. BSmooth() will compute smoothed values for the whole BSseq object, however. Hope that helps!