MethylGenotyper aims to call genotypes from three types of probes in Infinium methylation array: SNPs probes, Type I probes with SNPs at the extension bases causing color-channel-switching, and Type II probes with SNPs at the extension bases. By properly modeling the relationship between methylation intensity and SNP genotypes, MethylGenotyper can produce accurate genotypes for ~4000 SNPs from EPIC array and ~2000 SNPs from 450K array, enables accurate estimation of population structure and genetic relatedness. We have wrapped all these functions into MethylGenotyper and strongly encourage researchers to incorporate it into the EWAS pipeline to maximize statistical power and avoid spurious association signals.

Please read the vignette for detailed description and recommended workflow at vignette/vignette.pdf and the reference manual at vignette/MethylGenotyper_1.0.pdf.

library(devtools)
install_github("Yi-Jiang/MethylGenotyper")