Can MOABS include biological replicates for analysis?

[Fenheyue90]

Dear Dr. Sun,

I want to use MOABS to detect the DMRs between two groups with replicates. I read the MOABS manual (v.1.2.2), I found MOABS can only be used to detect DMRs between two samples. When I input the biological replicates through "-r" option, I found MOABS first merge these replicates into a single file, and use two merged files to detect DMRs, in this case, the biological variation is ignored. So how to incorporate the biological replicates in the analysis ? Or I miss something ?

Many thanks !