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Analyzing Methylome Data Using
Fabian MüllerEpigenomics 2016Puerto RicoFebruary 2, 2016
BeadsR I∩
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— Workflow
Analyzing Methylome Data Using RnBeads 2016-02-02
BeadsR I∩
Assenov, Müller, Lutsik, Walter, Lengauer, Bock (2014), Nature Methods, 11(11), 1138–1140
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BeadsR I∩ — Workflow
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Analyzing Methylome Data Using RnBeads
2016-02-02Analyzing Methylome Data Using RnBeads
Tutorial website:http://rnbeads.mpi-inf.mpg.de/tutorial.php
Hands-On
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System Requirements
• Windows, Linux, MacOS, …• Working installation of R (version 3.0 or higher)
§ Or admin rights in order to install R and ghostscript• ≥ 4 GB of main memory• ≥ 4 GB of free disk space• Internet connection
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Getting Started
• Visit the tutorial website:§ http://rnbeads.mpi-inf.mpg.de§ → Tutorial
• Download the tutorial scripts and data§ Download and unzip
• Install R• Install Ghostscript and RnBeads• Run your methylation analyses
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Vanilla Analysis
• Runs through the entire RnBeads workflow with specified analysis options
• Get started with 01_vanilla_Ziller450k.R1. Start R2. Load RnBeads3. Specify analysis options4. Run analysis
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Ziller, et al. (2011), PLoS Genetics, 7(12), e1002389
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Custom-Tailored Analysis
• Explore RnBeads modules, functions and classes• See examples in 02_step_by_step_Ziller450k.Rmd
§ With a few exceptions, examples for Illumina 450K array analysis generalize to bisulfite sequencing data
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Analyzing Bisulfite-Sequencing Data• Explore RnBeads modules,
functions and classes• Vanilla analysis
§ 03_vanilla_BockRRBS.R
• Custom analysis§ See examples in
04_step_by_step_BockRRBS.Rmd
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Bock, et al. (2012), Mol. Cell, 47(4), 633-647
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Performance Tuning
• Parallel computation§ foreach and doParallel packages
• Disk-based storage of large data matrices§ ff package
• Deploying RnBeads on a scientific computing cluster
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Beyond DNA Methylation
• Logging• HTML reports• See examples in
05_beyond_methylation.R
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Summary
• RnBeads …§ ... is an R package for start-to-finish DNA methylation analysis§ … enables large-scale analyses for virtually any methylation platform
providing basepair resolution (methylation arrays and bisulfite sequencing)§ … supports a wide range of input and export formats§ … performs analysis on individual CpGs as well as predefined or custom
genomic regions§ … generates informative and comprehensive HTML reports containing
method descriptions, publication grade plots and data tables§ … does not require expert knowledge to run§ … enables configurable for custom analysis due to its modular design and
programming interface
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On the Shoulders of Giants
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Acknowledgements
Analyzing Methylome Data Using RnBeads 2016-02-02
Pavlo LutsikKarl NordstrømJörn Walter
Yassen Assenov (MPII, DKFZ)Pavlo Lutsik (Saarland Univ.)Fabian Müller
BeadsR I∩
Felipe AlbrechtPeter EbertMarkus ListMichael SchererGeorg FriedrichJoachim BüchChristoph Bock (MPII, CeMM)Thomas Lengauer
http://rnbeads.mpi-inf.mpg.de
Deutsches Epigenom Programm
epigenomebl printUE
EU
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