Hello all, this is my first time working with methylation 450k data set and I have few beginner level questions. Our group is currently trying to study progression of a rare disease from mild to severe, with infinium 450K we are trying to understand if change in methylation or differential methylation can explain this progression. So my two groups are Mild and Severe. Our collaborator has already processed the data using the Methylumi package and has run some QC steps. The current data file that I am considering has variables like ID(cg*),p-value, beta and M-value, to calculate DMP/DMR what is the best variable to compare between two groups? I looked into Minfi package but it seems to get DMP/DMR I will have start from the beginning by processing the IDAT files.
Appreciate all you suggestion and comments.