# Quality control and analysis tools for Illumina DNA methylation BeadChip

## Documentation for package ‘ENmix’ version 1.40.2

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

## Help Pages

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.