First version of RAMEN. The following functions are implemented to conduct a genome-exposome contribution analysis to DNA methylome variability:
- findVMRs() identifies Variable Methylated Regions (VMRs) in microarrays
- summarizeVMRs()summarizes the regional methylation state of each VMR
- findCisSNPs() identifies the SNPs in cis of each VMR
- selectVariables() conducts a LASSO-based variable selection strategy to identify potentially relevant cis SNPs and environmental variables
- lmGE() fits linear single-variable genetic (G) and environmental (E), and pairwise additive (G+E) and interaction (GxE) linear models and select the best explanatory model per VMR.
- nullDistGE() simulates a delta R squared null distribution of G and E effects on DNAme variability. Useful for filtering out poor-performing best explanatory models selected by lmGE().