Horvath's Epigenetic Clock and Coefficients
Hello,
I am trying to implement and better understand the Horvath's epigenetic clock.
By now, so far, I have computed the beta values with my noob programming skills. To accomplish that I just used the minfi package available on the bioconductor.
Now, I have two problems, the first one is to understand what I have to do next;
the second problem regards to the fact that I can easily compute (without understanding) the Horvath clock by implementing the wateRmelon package using the agep function, however, I would like to determine the Horvath Coefficients on my own.
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Your goals are not very clear. 1) You arrived at your beta values, but what is the objective of your analysis? That question is not related to the actual programming, because there is not a single "next step". Is your goal to compare methylation values between experimental groups, for example? 2) Horvath's clock is a mathematical model with which you calculate an epigenetic age by using specific coefficients. Horvath derived the coefficients from the analysis of 1000s of arrays. Thus, after validation in multiple tissues, they are applicable to other data, such as your data. The coefficients are what they are, if you estimated other coefficients you would be creating a different clock. So you should use them to predict epigenetic age on your samples. It doesn't look like your goal is to create a new clock.