I have been looking at dmpFinder function, and I was wondering if the function could work with beta values (as a matrix) and phenotypes (as a vector, for example race) without having the methylset or methylation object. My only worry is that how the function would be able to match the correct phenotypes to correct sample id beta values. Since the sample IDs are columns in the beta matrix, I am not sure what to do. Any suggestions would be appreciated. Thank you!

The help page is helpful for answering your question:

Usage:

     dmpFinder(dat, pheno, type = c("categorical", "continuous"),
         qCutoff = 1, shrinkVar = FALSE)

Arguments:

     dat: A 'MethylSet' or a 'matrix'.

   pheno: The phenotype to be tested for association with methylation.

The expectation will be that you have samples in columns and beta values (ordered along the genome) in columns. The phenotypic data is also assumed to be in the same order as the columns of your matrix.