Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
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DOI：
10.1093/bioinformatics/btu049
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发表时间：
2014-05-15
期刊：
影响因子：
5.8
通讯作者：
Irizarry, Rafael A.
中科院分区：
文献类型：
--
作者：
Aryee, Martin J.;Jaffe, Andrew E.;Irizarry, Rafael A.
动机：最近发布的Infinium HumanMethylation 450阵列（“450k”阵列）提供了一种高通量检测方法，可以在一系列基因组特征中的450000个位点上定量DNA甲基化（DNAm）。虽然比高通量测序为基础的技术不太全面，这种产品是更具成本效益，并有望成为最广泛使用的DNAm高通量测量技术在未来几年。结果：在这里，我们描述了一套计算工具，将国家的最先进的统计技术的DNAm数据的分析。该软件的结构可以很容易地适应未来版本的技术。我们包括方法预处理，质量评估和检测差异甲基化的区域从酶的兆规模。我们展示了我们的软件如何为未来的方法提供强大而灵活的开发平台。我们还说明了我们的方法如何使技术，使发现以前认为是可能的，只有基于测序的方法。
Motivation: The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at similar to 450000 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.