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Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Bioconductor version: Release (3.19)

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) .

Author: Andrey A Shabalin [aut, cre] , Shaunna L Clark [aut], Mohammad W Hattab [aut], Karolina A Aberg [aut], Edwin J C G van den Oord [aut]

Maintainer: Andrey A Shabalin <andrey.shabalin at>

Citation (from within R, enter citation("ramwas")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Overview HTML R Script
2. CpG sets HTML R Script
3. BAM Quality Control Measures HTML R Script
4. Joint Analysis of Methylation and Genotype Data HTML R Script
5.a. Analyzing Illumina Methylation Array Data HTML R Script
5.c. Analyzing data from other sources HTML R Script
6. RaMWAS parameters HTML R Script
Reference Manual PDF


biocViews BatchEffect, Coverage, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, PrincipalComponent, QualityControl, Sequencing, Software, Visualization
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License LGPL-3
Depends R (>= 3.3.0), methods, filematrix
Imports graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics
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Suggests knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805
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Source Package ramwas_1.28.0.tar.gz
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macOS Binary (x86_64) ramwas_1.28.0.tgz
macOS Binary (arm64) ramwas_1.28.0.tgz
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