Question: how to find differentially methylated regions (for example with probe lasso in Champ) based on regression continuous variable ~ beta (with CpGassoc)
1
gravatar for Line Heylen
3.5 years ago by
Line Heylen10
Belgium
Line Heylen10 wrote:

Hi,


I performed 450K Illumina methylation chips on human samples, and want to search for the association between a continuous variable and beta, adjusted for other covariates. For this, I used the CpGassoc package in R. I would also like to search for differentially methylated regions based on the significant CpG sites. However, the probe lasso function in the Champ package and also other packages for 450K DMR analyses always assume 2 groups for which DMRs needs to be find. I do not have 2 groups, but this continuous variable. Is there a way in load my output from CpGassoc in the probe lasso function from Champ? Or into another bump hunter package? I'm a MD, not a bio-informatician, thus comb-p etc. is not possible for me. 

Thank you very much for your help.


Kind regards,
Line

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