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

TitleMinfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Publication TypeJournal Article
AuthorsAryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA
Aged, algorithms, Colonic Neoplasms, DNA Methylation, Genome, High-Throughput Nucleotide Sequencing, HUMANS, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, software

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.

PubMed ID24478339
PubMed Central IDPMC4016708
Grant ListGM083084 / GM / NIGMS NIH HHS / United States
GM103552 / GM / NIGMS NIH HHS / United States
P50HG003233 / HG / NHGRI NIH HHS / United States
R01 GM083084 / GM / NIGMS NIH HHS / United States
R01AG042187 / AG / NIA NIH HHS / United States