# Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

## Documentation for package ‘ENmix’ version 1.25.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'