RaMWAS: fast methylome-wide association study pipeline for enrichment platforms.
Ontology highlight
ABSTRACT: 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.
SUBMITTER: Shabalin AA
PROVIDER: S-EPMC6022807 | biostudies-literature | 2018 Jul
REPOSITORIES: biostudies-literature
Publications
RaMWAS: fast methylome-wide association study pipeline for enrichment platforms.
Shabalin Andrey A AA Hattab Mohammad W MW Clark Shaunna L SL Chan Robin F RF Kumar Gaurav G Aberg Karolina A KA van den Oord Edwin J C G EJCG
Bioinformatics (Oxford, England) 20180701 13
<h4>Motivation</h4>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.<h4>Results</h4>We present a Bioconductor R package called RaMWAS with a full set of tools ...[more]
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