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DOI: 10.18129/B9.bioc.ramwas    

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Bioconductor version: Release (3.5)

RaMWAS provides 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.

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 <ashabalin at>

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HTML R Script 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. Analyzing data from other sources
HTML R Script 6. RaMWAS parameters
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, Coverage, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, PrincipalComponent, QualityControl, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (0.5 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
Suggests knitr, rmarkdown, pander, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37, BSgenome.Ecoli.NCBI.20080805
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