I am working with WGBS data, There I am using MethylKit package for DMC analysis. Differential DNA methylation is usually calculated by comparing the proportion of methylated Cs in a test sample relative to a control. In simple comparisons between such pairs of samples (i.e. test and control), methods such as Fisher’s exact test can be used. When there is only one sample per sample group, calculateDiffMeth() automatically applies Fisher’s exact test.
My question is as Fisher’s exact test has some limitations (DOI: 10.1093/nar/gku154), can Wald test be done using Methylkit?