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


METHODS
http://bioconductor.org/packages/release/bioc/html/minfi.html.


BACKGROUND
khansen@jhsph.edu; rafa@jimmy.harvard.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, Department of Computer Science, University of Maryland, College Park, MD 20742, USA, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Martin J
MJ
Aryee
Andrew E
AE
Jaffe
Hector
H
Corrada-Bravo
Christine
C
Ladd-Acosta
Andrew P
AP
Feinberg
Kasper D
KD
Hansen
Rafael A
RA
Irizarry
D000368:Aged; D000465:Algorithms; D003110:Colonic Neoplasms / Q000235:genetics; D019175:DNA Methylation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software