Quality control and analysis tools for Illumina DNA methylation BeadChip

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Documentation for package ‘ENmix’ version 1.44.3

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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"'
methscore DNA Methylation predictors
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
rcp2 Modified RCP method
readidat Parsing IDAT files for Illumina methylation arrays .
readmanifest Parsing Illumina methylation arrays manifest file.
relic REgression on Logarithm of Internal Control probes (RELIC)
repicc Calculating intraclass correlation coefficient using replicate samples
rgDataSet Class '"rgDataSet"'
rgDataSet-class Class '"rgDataSet"'
rm.cgsuffix Remove suffix from CpG names and combine duplicated CpGs
show-method Class '"methDataSet"'
show-method Class '"rgDataSet"'
simubed Simulation of bed format example file.