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shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.

Authors :
Fortin JP
Fertig E
Hansen K
Source :
F1000Research [F1000Res] 2014 Jul 30; Vol. 3, pp. 175. Date of Electronic Publication: 2014 Jul 30 (Print Publication: 2014).
Publication Year :
2014

Abstract

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.

Details

Language :
English
ISSN :
2046-1402
Volume :
3
Database :
MEDLINE
Journal :
F1000Research
Publication Type :
Academic Journal
Accession number :
25285208.2
Full Text :
https://doi.org/10.12688/f1000research.4680.2