M value or beta value? - Githubissues

lissettegomez / coMethDMR

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M value or beta value? #3

Closed ggzheng closed 4 years ago

ggzheng commented 4 years ago

Hi,

I saw you mentioned that "there are two main steps in coMethDMR: (1) identifying comethylatyed clusters (2) testing methylation levels in those comethylated clusters against a phenotype".

In step 1 and 2, should we use beta value or M values for CoMethDMR?

Thanks!

ggzheng commented 4 years ago

I double checked documents. I think it should use M values in step 1 and 2.

gabrielodom commented 4 years ago

Hi Yuanchao, please forgive us for taking so long to reply. We are quite busy with grants and the COVID-19 response in our region. It appears that you were able to find an answer, but please do not hesitate to reopen this issue if you get stuck again :)

ggzheng commented 4 years ago

No worry. I noticed it uses M values, but the input for step 1 could be either beta or M, but the input for step 2 should be the beta matrix. That's what I found.