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

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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.

Author
Zongli Xu [cre, aut], Liang Niu [aut], Leping Li [ctb], Jack Taylor [ctb]
Date of publication
None
Maintainer
Zongli Xu <xuz@niehs.nih.gov>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

Man pages

bmiq.mc
A multi-processor wrapper of BMIQ method
ComBat.mc
A multi-processor wrapper for ComBat method.
ctrlsva
Non-negative control surrogate variables
freqpoly
Frequency polygon plot
multifreqpoly
Frequency polygon plot to display data distribution.
nmode.mc
Estimating number of mode in methylaion data for each probe.
normalize.quantile.450k
Quantile normalization.
norm.quantile
Quantile normalization.
oxBS.MLE
oxBS-MLE.
pcrplot
Principal component regression plot
plotCtrl
Plot internal controls of 450K or MethylationEPIC BeadChip.
preprocessENmix
The ENmix background correction for HumanMethylation 450 and...
QCfilter
Sample or CpG probe filter.
QCinfo
QC information.
rcp
Regression on Correlated Probes(RCP)
relic
RELIC dye bias correction methodfor Illumina...
rm.outlier
Filtering out outlier and/or low quality values

Files in this package

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