shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.
shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.
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DOI：
10.12688/f1000research.4680.1
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发表时间：
2014-01-01
期刊：
影响因子：
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通讯作者：
Hansen, Kasper
中科院分区：
文献类型：
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作者：
Fortin, Jean-Philippe;Fertig, Elana;Hansen, Kasper
我们推出了shinyMethyl，这是一个Bioconductor包，用于对Illumina 450 k阵列的DNA甲基化数据进行交互式质量控制。该软件包将450k个实验总结为可导出的小R对象，并从其中启动交互式界面。反应性图允许对样品进行快速和直观的质量控制评估。此外，探索的表型协会是可能的，通过着色和主成分分析。总而言之，该软件包可以轻松地对大规模甲基化数据集进行质量评估，例如表观基因组关联研究或通过癌症基因组图谱门户网站提供的数据集。shinyMethyl包在R中实现，可通过Bioconductor获得。其开发存储库位于https://github.com/jfortin1/shinyMethyl。
We present shinyMethyl, a Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an interactive interface is launched. Reactive plots allow fast and intuitive quality control assessment of the samples. In addition, exploration of the phenotypic associations is possible through coloring and principal component analysis. Altogether, the package makes it easy to perform quality assessment of large-scale methylation datasets, such as epigenome-wide association studies or the datasets available through The Cancer Genome Atlas portal. The shinyMethyl package is implemented in R and available via Bioconductor. Its development repository is at https://github.com/jfortin1/shinyMethyl.