What is MethylAction?

MethylAction is an R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide. These techniques include MBD-isolated Genome Sequencing (MiGS), MBD-seq, and MeDIP-seq.

Key Features:

• Designed for studies investigating biological and disease sub-types
• Supports comparisons between more than 2 groups (up to 8 tested by authors)
• Computes statistical significance across genomic regions
• Stratifies groups by consistency ("frequent" and "other" DMRs)
• Performs bootstrapping or permutations to establish false discovery rates (FDRs)
• Provides tools for visualization (heatmaps and karyograms)

How to Use MethylAction

We have created a step-by-step how to for new users to learn the essential functions of the R package and perform an analysis on example data.

Step-by-Step How To:

• View Online
• Download PDF
• Download DOCX
• Download demo data for the above HowTos (methylaction_demo.tar.gz)

For more advanced options, please refer to the function manual. This information is also available from within R using the "?" command.

Function and Reference Manuals:

• Download Function Reference PDF
• Download DMR Output Column Description XLSX
• Download "ma" List Object Element Description XLSX

Citation

Please refer to our open access manuscript to learn more about MethylAction. Please cite this work if MethylAction is useful in your research.

Bhasin, JM, Hu, B, and Ting, AH. (2016). MethylAction: detecting differentially methylated regions that distinguish biological subtypes. Nucleic Acids Res. 44, 106-116. PMID: 26673711. PMCID: PMC4705678.

Contact and Help

Please open an issue on the MethylAction GitHub Issues page for questions, bug reports, or enhancement requests.

You may also contact the package author with questions or feedback: