R packages for DNA methylation as mediator analysis

Question

[Bioinfonext]

Hi,

I do have diabetes and no diabetes disease phenotypes, and also arsenic exposure and DNA methylation data (epic array). Could you please suggest best way to find CpG sites associated with arsenic exposure and diabetes. We know that toxic element leads to health risk but we want to study this by using DNA methylation as mediator for disease risk.

Could you please suggest any R package for doing these types of analysis. I have used previously limma for toxic element exposure and DNA methylation association analysis but not sure how make connections with health risk phenotype?

Many thanks,

[LChart]

I think you need to be a little bit clearer about the structure of your data. You have measured DNA methylation from (what tissue?) in how many diabetic (type 2?) and non-diabetic patients; and what metadata have you collected for each patient? Does this metadata include arsenic exposure?

[Bioinfonext]

Thanks, we measured blood DNA methylation using epic array in 100 no-diabetic and 100 type 1 diatbetic patients matched for age, sex and smoking and also measured arsenic exposure using ICP-MS.