Metheor only calculate methylation diversity based on CpG site？

[feihongloveworld]

Metheor only calculate methylation diversity based on CpG site？

[dohlee]

Yes, it considers only CpG sites.

[feihongloveworld]

but MHL was designed on MHB which contain more than 3 CpG sits. so I'm wondering weather MHLs based on a CpG sits are different with MHLs based on MHB

[dohlee]

That's right. MHL was designed for a genomic region in the original paper, but CpG-wise MHL was then proposed in Scherer et al., 2020, which is the benchmark paper for Metheor. Please refer to https://doi.org/10.1093/nar/gkaa120. Basically, you can think that a set of sequencing reads covering each CpG defines the genomic region considered for MHL calculation.

[feihongloveworld]

I read Scherer's paper just now. whether PM and ME only are calculated based on the 4-CpG window? if the CpG number is more than 4 in a block, should I use overlapped windows with step 1 to get PM and ME?

[dohlee]

Yes, PM and ME values are assigned for four consecutive CpGs (i.e. CpG quartets). If you want to compute PM and ME in certain genomic block, you can simply average all PM/ME values for CpG quartets overlapping with that genomic block.