Introduction

The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years.Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods.http://bioconductor.org/packages/release/bioc/html/minfi.html.khansen@jhsph.edu; rafa@jimmy.harvard.eduSupplementary data are available at Bioinformatics online.

Publications

  1. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
    Cite this
    Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA, 2014-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Martin J Aryee
    Developer

    Department of Pathology, Massachusetts General Hospital and Harvard Medical School, United States of America

  2. Andrew E Jaffe
    Developer

  3. Hector Corrada-Bravo
    Developer

  4. Christine Ladd-Acosta
    Developer

  5. Andrew P Feinberg
    Developer

  6. Kasper D Hansen
    Developer

  7. Rafael A Irizarry
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT001527
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByRafael A Irizarry