Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

Documentation for package ‘ENmix’ version 1.25.1

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B2M	Convert methylation beta value to M value.
calcdetP	To calculate detection P values
combp	Identification of differentially methylated regions
ctrlsva	Non-negative internal control surrogate variables
dupicc	Evaluations of methylation duplicates
estimateCellProp	Cell type proportion estimation
freqpoly	Frequency polygon plot
getB	Extract methylation Beta values.
getCGinfo	CpG probe annotation inforamtion
getmeth	Create a methDataSet
ipdmr	Differentially methylated region finder using interval P values
M2B	Convert methylation M value to methylation beta value.
methDataSet	Class '"methDataSet"'
methDataSet-class	Class '"methDataSet"'
methyAge	Methylation Age estimation
mhtplot	P value manhattan plot
mpreprocess	methylation QC and preprocessing pipeline for Illuminal arrays
multifreqpoly	Frequency polygon plot
nmode.mc	Estimating number of mode for each row of data
norm.quantile	Quantile normalization.
normalize.quantile.450k	Quantile normalization.
oxBS.MLE	oxBS-MLE.
p.qqplot	P value Q-Q plot
pcrplot	Principal component regression plot
plotCtrl	Internal control plot
predSex	Estimating sample sex
preprocessENmix	The ENmix background correction for HumanMethylation 450 and MethylationEPIC BeadChip
QCfilter	Sample or CpG probe filter.
QCinfo	QC information
rcp	Regression on Correlated Probes(RCP)
readidat	Parsing IDAT files from Illumina methylation arrays.
readmanifest	Parsing Illumina methylation arrays manifest file.
relic	RELIC dye bias correction method for Illumina HumanMethylation450 and MethylationEPIC BeadChip
rgDataSet	Class '"rgDataSet"'
rgDataSet-class	Class '"rgDataSet"'
rm.outlier	Filtering out outlier and/or low quality values
show-method	Class '"methDataSet"'
show-method	Class '"rgDataSet"'