I've downloaded two MeDIP-Seq datasets from the same patient (Normal tissue, Cancer tissue) and I want to identifie differentially methylated regions between those datasets.
I pre-processed my datasets, I made the alignment step using BWA and now I'm in the MEDIPS part. I am following this tutorial http://www.bioconductor.org/packages/release/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf I made every single step until chapter 6. I'm know having trouble finding the way to proceed to the DMR analysis.
Let's assume that my bam file names after BWA alignment are normal_tissue.bam and cancer_tissue.bam !
If you look at the above link, chapter 6, you'll see that they are using more replicates so I can't really understand what am I supposed to do with my two BAM files. Also I can't really understand what they mean with things like: MEDIPS SET, INPUT SETS and Cset.
Can anyone make any R coding suggestions based on my BAM file names and the above tutorial (chapter 6) ?
I'm totally new in the field of bioinformatics so any comment would be very helpful!
Thank you very much.