MethylAid: Visual and interactive quality control of large Illumina DNA Methylation array data sets

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Author
Maarten van Iterson [aut, cre], Elmar Tobi[ctb], Roderick Slieker[ctb], Wouter den Hollander[ctb], Rene Luijk[ctb] and Bas Heijmans[ctb]
Date of publication
None
Maintainer
M. van Iterson <mviterson@gmail.com>
License
GPL (>= 2)
Version
1.8.0
URLs

View on Bioconductor

Man pages

as.background
generate background data
combine-summarizedData-ANY-method
concatenates two summarizedData objects into one object
exampleData
summarizedData object on 500 450k Human Methylation samples
summarize
summarization of Illumina Human DNA Methylation array data
summarizedData-class
container for summarized Illumina Human DNA Methylation array...
summarizedData-methods
show method for Illumina Human DNA Methylation array data
visualize
visualize the summarized Illumina Human DNA Methylation array...

Files in this package

MethylAid/DESCRIPTION
MethylAid/NAMESPACE
MethylAid/R
MethylAid/R/filterControlPlots.R
MethylAid/R/qualityControlPlots.R
MethylAid/R/replaceZeros.R
MethylAid/R/server.R
MethylAid/R/summarization.R
MethylAid/R/summarizeControls.R
MethylAid/R/summarizedData.R
MethylAid/R/ui.R
MethylAid/R/uitext.R
MethylAid/R/util.R
MethylAid/R/visualization.R
MethylAid/build
MethylAid/build/vignette.rds
MethylAid/data
MethylAid/data/datalist
MethylAid/data/exampleData.RData
MethylAid/inst
MethylAid/inst/CITATION
MethylAid/inst/MethylAid
MethylAid/inst/MethylAid/global.R
MethylAid/inst/MethylAid/server.R
MethylAid/inst/MethylAid/ui.R
MethylAid/inst/doc
MethylAid/inst/doc/MethylAid.R
MethylAid/inst/doc/MethylAid.Rnw
MethylAid/inst/doc/MethylAid.pdf
MethylAid/inst/scripts
MethylAid/inst/scripts/config.R
MethylAid/inst/scripts/sge.tmpl
MethylAid/inst/scripts/summarize.R
MethylAid/inst/scripts/summarize.sh
MethylAid/inst/unitTests
MethylAid/inst/unitTests/test_summarize.R
MethylAid/inst/unitTests/test_visualize.R
MethylAid/inst/www
MethylAid/inst/www/About.html
MethylAid/man
MethylAid/man/as.background.Rd
MethylAid/man/combine-summarizedData-ANY-method.Rd
MethylAid/man/exampleData.Rd
MethylAid/man/summarize.Rd
MethylAid/man/summarizedData-class.Rd
MethylAid/man/summarizedData-methods.Rd
MethylAid/man/visualize.Rd
MethylAid/tests
MethylAid/tests/runTests.R
MethylAid/vignettes
MethylAid/vignettes/MethylAid.Rnw
MethylAid/vignettes/MethylAid.bib
MethylAid/vignettes/screenshot_MethylAid.png