minfi package, DMRs,

Question

[niutster]

Hi all,

I have a idat file contains three types of experiment: control, patient and suspected people, i want to find DMRs between patient and control data but in minfi when you read the data completely and map them on the genome you cant seperate them in bumphunter(function that finds DMRs), How can i find DMRs between two desired data?

Answer 1

[igor]

You can use bumphunter to detect genomic regions that are differentially methylated between two conditions. If you have three conditions, subset the experiment to only contains the samples from the two conditions of interest.

[niutster]

How can I do it? Could you explain?