What should be the coef in cpg.annotate if my intereste is "Condition". In bumphunting the coef is 2 as it calls for the column number of designmatrix. But in dmrcate manual I saw it to be index. So is it that my coef=1?

I am not sure what you mean by 'I saw it to be index', but you can be sure that the dmrcate manual doesn't indicate that you should use the intercept column. The coef argument is how you specify which coefficient you are interested in testing, so in your case it would be coef=2.

Thanks james for the answer. In the dmrcate manual under the cpg.annoate its as follows "coef The column index in design corresponding to the phenotype comparison."

Thanks james for the answer. In the dmrcate manual under the cpg.annoate its as follows "

coef The column index in design corresponding to the phenotype comparison."Right. I could translate that to be 'the column number of your design matrix that contains the coefficient you care about'. Does that make more sense?