Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Motivation: 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...

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Bibliographic Details
Published in:Bioinformatics Vol. 30; no. 10; pp. 1363 - 1369
Main Authors: Aryee, Martin J., Jaffe, Andrew E., Corrada-Bravo, Hector, Ladd-Acosta, Christine, Feinberg, Andrew P., Hansen, Kasper D., Irizarry, Rafael A.
Format: Journal Article
Language:English
Published: England Oxford University Press 15.05.2014
Subjects:
Aged
Algorithms
Colonic Neoplasms - genetics
DNA Methylation
Genome
High-Throughput Nucleotide Sequencing - methods
Humans
Oligonucleotide Array Sequence Analysis - methods
Original Papers
Polymorphism, Single Nucleotide
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary:Motivation: 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. Results: 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. Availability and implementation: http://bioconductor.org/packages/release/bioc/html/minfi.html. Contact: khansen@jhsph.edu; rafa@jimmy.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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SourceType-Scholarly Journals-1
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Department of Biostatistics, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA.
Present address: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
Associate Editor: Alfonso Valencia
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btu049