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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. 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?

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