Motivation: Enrichment-based technologies can provide measurements of DNA methylation at tens of millions of CpGs for thousands of samples. Existing tools for methylome-wide association studies cannot analyze datasets of this size and lack important features like principal component analysis, combined analysis with SNP data and outcome predictions that are based on all informative methylation sites.
Results: We present a Bioconductor R package called RaMWAS with a full set of tools for large-scale methylome-wide association studies. It is free, cross-platform, open source, memory efficient and fast.
Availability and implementation: Release version and vignettes with small case study at bioconductor.org/packages/ramwas Development version at github.com/andreyshabalin/ramwas.
Supplementary information: Supplementary data are available at Bioinformatics online.