I'm doing some analysis on 850K data. I have downloaded data from GSE110555.
It's every nice that I found a matrix file from GSE110555, the data format like bellow.
ID_REF R01C01_U R01C01_M R01C01_Pval R03C01_U R03C01_M R03C01_Pval
cg00012701 5853 396 0 6781 582 0
cg00019576 228 12808 0 359 14697 0
Every sample has 3 columns, the 1st is Unmethylated signal, 2nd is Methylated signal and 3rd is Detection Pval.
Here I have three questions.
- For computing methylation level, I just using beta value formula M/(U+M+100) for single locus and regions, is it right?
- How to find DMR based on this matrix? I can analysis WGBS based on R package bsseq, but it cannot be used for 850K data.
- How to link ID_REF(the first column above, like cg00012701) and genome position?
Thank you very much!