I am trying to use RnBeads to analyze DNA-methylation data, but I already have a matrix of beta-values. I cannot find a way to import data in that format and launch a differential analysis.
Has anyone encountered the same problem?
As a warning, this code that I wrote may be slightly outdated.
However, if you have the raw .idats (which I think is important: if possible, I think testing different normalizations can give you a better feel for the robustness of your results), I think this code using a benchmark (described here) with some methods may also help as a starting point?