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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Published in | Bioinformatics Vol. 30; no. 10; pp. 1363 - 1369 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
15.05.2014
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Subjects | |
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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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 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 |