I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with eGFR has been showed through regression analysis but I am not sure how to run regression for so many CpG probes in R.

Can you have look on this below publication and could you help with R code for regression analysis?


I do have methylation beta value from RnBeads but I am not sure how to read methylation data (rows/column-CpG/SampleID) and then how to read phenotype data file and finally how to make single sheet to run regression analysis?

  • $\begingroup$ Have a look at this method academic.oup.com/bioinformatics/article/34/15/2657/4939328 $\endgroup$
    – user438383
    Commented May 13, 2022 at 15:27
  • $\begingroup$ Hi, I found a way to do methylation data association analysis with eGFR as shown here (support.bioconductor.org/p/93868), but not sure how make input files; like in methylation data file; do I take CpG probe as rows or column? and I am also not sure how to mention covarites in modal.matrix for eGFR association? Many thanks $\endgroup$ Commented May 16, 2022 at 10:26

1 Answer 1


Answer from @user4939328, converted from comment. Please improve this answer if you can:

Have a look at this method:


[Wondering why this was converted from a comment? See the StackExchange rules about comments here]


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.