Answers.Body: <p><em>Answer from @user4939328, converted from comment. Please improve this answer if you can:</em></p>
  <p>Have a look at this method:</p>
  <p><a href="https://academic.oup.com/bioinformatics/article/34/15/2657/4939328" rel="nofollow noreferrer">https://academic.oup.com/bioinformatics/article/34/15/2657/4939328</a></p>
  <p><em>[Wondering why this was converted from a comment? See the StackExchange rules about comments <a href="https://bioinformatics.stackexchange.com/help/privileges/comment">here</a>]</em></p>
  
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Answers.CreationDate: 2022-05-15T05:45:30.180Z
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Answers.UserDisplayName: gringer
Body: <p>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.</p>
  <p>Can you have look on this below publication and could you help with R code for regression analysis?</p>
  <p><a href="https://www.nature.com/articles/s41467-017-01297-7.pdf" rel="nofollow noreferrer">https://www.nature.com/articles/s41467-017-01297-7.pdf</a></p>
  <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-13T15:27:04.800Z
Comments.Text: Have a look at this method https://academic.oup.com/bioinformatics/article/34/15/2657/4939328
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-16T10:26:09.017Z
Comments.Text: Hi, I found a way to do methylation data association analysis with eGFR as shown here (https://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
Comments.UserDisplayName: bioinfonext
Tags: <bioconductor><r><epigenetics>
Title: Association analysis for methylation beta value and phenotypes in R
ThreadText: # Association analysis for methylation beta value and phenotypes in R
  
  (Asked by: username_0 on 2022-05-13)
  
  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?
  
  **Tags:** bioconductor, r, epigenetics
  
  > **Comments:**
  > **username_1**: Have a look at this method https://academic.oup.com/bioinformatics/article/34/15/2657/4939328  
  > **username_0**: Hi, I found a way to do methylation data association analysis with eGFR as shown here (https://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  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-05-15. Score: -1
  
  *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](https://bioinformatics.stackexchange.com/help/privileges/comment)]*
  
  
  ---
  
  