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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?

https://www.nature.com/articles/s41467-017-01297-7.pdf

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?

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

Have a look at this method:

https://academic.oup.com/bioinformatics/article/34/15/2657/4939328

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

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