RRBS data analysis using Bismark and methylkit

Question

[Arindam Ghosh]

Once we have read in the cytosine report files with methRead(), how to generate a table/dataframe of beta values or equivalent for all samples as columns and CpG sites as rows? Is the percMethylation() function the correct function to use? Beta values I guess are from microarray, is percent-methylation the correct equivalent?

[Papyrus]

You can actually divide the C counts by the total counts (C+T) to get methylation percentages. I have never used that particular function percMethylation(), but you can check the 2 approaches and see if they return you the same values.

Regarding the nomenclature, yes, "beta value" is array terminology, and I would not use it for bisulfite sequencing data. For sequencing data, in the literature you usually see a variety of terms such as "methylation value", "methylation percentage", etc. And people use both the [0,100] and [0,1] scales, so it is up to you (there's not much difference).