Quality control and analysis tools for Illumina DNA methylation BeadChip

Documentation for package ‘ENmix’ version 1.26.10

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B2M	Converting 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	Evaluation of measurement reliability using duplicate samples
estimateCellProp	Cell type proportion estimator
freqpoly	Frequency polygon plot
getB	Extract methylation Beta values.
getCGinfo	CpG probe annotation inforamtion
getmeth	Create a methDataSet
ipdmr	Differentially methylated regions
M2B	Converting methylation M value to beta value.
methDataSet	Class '"methDataSet"'
methDataSet-class	Class '"methDataSet"'
methyAge	Methylation Age estimator
mhtplot	P value manhattan plot
mpreprocess	methylation data QC and preprocessing pipeline for Illuminal BeadChips
multifreqpoly	Multiple frequency polygon plot
nmode	Estimating number of mode for each row of data
norm.quantile	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
qcfilter	Filtering out low quality and outlier data
QCinfo	Extract QC information
rcp	Illumina methylation array probe type bias correction
readidat	Parsing IDAT files for Illumina methylation arrays .
readmanifest	Parsing Illumina methylation arrays manifest file.
relic	REgression on Logarithm of Internal Control probes (RELIC)
rgDataSet	Class '"rgDataSet"'
rgDataSet-class	Class '"rgDataSet"'
show-method	Class '"methDataSet"'
show-method	Class '"rgDataSet"'
simubed	Simulation of bed format example file.