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Bigmelon: Tools for analysing large DNA methylation datasets

Research output: Contribution to journalArticle

Tyler J. Gorrie-Stone, Melissa C. Smart, Ayden Saffari, Karim Malki, Eilis Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C. Schalkwyk

Original languageEnglish
Pages (from-to)981-986
Number of pages6
JournalBIOINFORMATICS
Volume35
Issue number6
Early online date23 Aug 2018
DOIs
Accepted/In press20 Aug 2018
E-pub ahead of print23 Aug 2018
Published15 Mar 2019

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Abstract

Motivation The datasets generated by DNA methylation analyses are getting bigger. With the release of the HumanMethylationEPIC micro-array and datasets containing thousands of samples, analyses of these large datasets using R are becoming impractical due to large memory requirements. As a result there is an increasing need for computationally efficient methodologies to perform meaningful analysis on high dimensional data. Results Here we introduce the bigmelon R package, which provides a memory efficient workflow that enables users to perform the complex, large scale analyses required in epigenome wide association studies (EWAS) without the need for large RAM. Building on top of the CoreArray Genomic Data Structure file format and libraries packaged in the gdsfmt package, we provide a practical workflow that facilitates the reading-in, preprocessing, quality control and statistical analysis of DNA methylation data. We demonstrate the capabilities of the bigmelon package using a large dataset consisting of 1193 human blood samples from the Understanding Society: UK Household Longitudinal Study, assayed on the EPIC micro-array platform. copy; 2018 The Author(s). Published by Oxford University Press.

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