ENmix: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

Illumina Methylation BeadChip array measurements have intrinsic levels of background noise that degrade methylation measurement. The ENmix package provides an efficient data pre-processing tool designed to reduce background noise and improve signal for DNA methylation estimation. Several efficient novel methods were incorporated in the package: ENmix is a model based background correction method that can significantly improve accuracy and reproducibility of methylation measures; RCP taking advantage of the high spatial correlation of DNA methylation levels between nearby type I and II probe pairs to reduce probe type bias and improve data quality on type II probe measures.The data structure used by the ENmix package is compatible with several other related R packages, such as minfi, wateRmelon and ChAMP, providing straightforward integration of ENmix-corrected datasets for subsequent data analysis. The software is designed to support large scale data analysis, and provides multi-processor parallel computing wrappers for some commonly used but computation intensive data preprocessing methods. In addition ENmix package has selectable complementary functions for efficient data visualization (such as data distribution plotting), quality control (identification and filtering of low quality data points, samples, probes, and outliers, along with imputation of missing values), inter-array normalization (3 different quantile normalizations), identification of probes with multimodal distributions due to SNPs and other factors, and exploration of data variance structure using principal component regression analysis plots. Together these provide a set of flexible and transparent tools for preprocessing of EWAS data in a computationally-efficient and user-friendly package.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")
AuthorZongli Xu [cre, aut], Liang Niu [aut], Leping Li [ctb], Jack Taylor [ctb]
Bioconductor views BatchEffect DNAMethylation DataImport MethylationArray Microarray Normalization OneChannel Preprocessing PrincipalComponent QualityControl Regression TwoChannel
Date of publicationNone
MaintainerZongli Xu <xuz@niehs.nih.gov>
LicenseArtistic-2.0
Version1.12.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/ComBat.mc.R R/QCfilter.R R/QCinfo.R R/bmiq.mc.R R/ctrlsva.R R/multifreqpoly.R R/nmode.mc.R R/norm.quantile.R R/normalize.quantile.450k.R R/oxBS.MLE.R R/pcrplot.R R/plotCtrl.R R/preprocessENmix.R R/rcp.R R/relic.R R/rm.outlier.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/ENmix.R
inst/doc/ENmix.Rnw
inst/doc/ENmix.pdf
inst/oxBS.MLE.RData
inst/testData
inst/testData/testData.R
inst/testData/testData.out
inst/unitTests
inst/unitTests/testDigests.rda
inst/unitTests/test_enmix.R
man
man/ComBat.mc.Rd man/QCfilter.Rd man/QCinfo.Rd man/bmiq.mc.Rd man/ctrlsva.Rd man/freqpoly.Rd man/multifreqpoly.Rd man/nmode.mc.Rd man/norm.quantile.Rd man/normalize.quantile.450k.Rd man/oxBS.MLE.Rd man/pcrplot.Rd man/plotCtrl.Rd man/preprocessENmix.Rd man/rcp.Rd man/relic.Rd
man/resultsChamp
man/resultsChamp/failedSample.txt
man/resultsChamp/raw_SampleCluster.jpg
man/resultsChamp/raw_densityPlot.pdf
man/resultsChamp/raw_mdsPlot.pdf
man/rm.outlier.Rd
tests
tests/runTests.R
vignettes
vignettes/ENmix.Rnw
vignettes/fig
vignettes/fig/BISULFITE_CONVERSION_I.jpg
vignettes/fig/NEGATIVE.jpg
vignettes/fig/NON-POLYMORPHIC.jpg
vignettes/fig/NORM_ACGT.jpg
vignettes/fig/dist.jpg
vignettes/fig/pcr_diag.jpg

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