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

## Documentation for package ‘ENmix’ version 1.14.0

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

## Help Pages

B2M | Convert Beta value to M value.
bmiq.mc | A multi-processor wrapper of BMIQ method
ComBat.mc | A multi-processor wrapper for ComBat method.
ctrlsva | Non-negative control surrogate variables
freqpoly | Frequency polygon plot
getBeta | Extract Beta value.
M2B | Convert M value to Beta value.
mpreprocess | A pipeline to perform background correction, dye bias correction, inter-array normalization and probe type bias correction for HumanMethylation 450 and MethylationEPIC BeadChip data.
multifreqpoly | Frequency polygon plot to display data distribution.
nmode.mc | Estimating number of mode in methylaion data for each probe.
norm.quantile | Quantile normalization.
normalize.quantile.450k | Quantile normalization.
oxBS.MLE | oxBS-MLE.
pcrplot | Principal component regression plot
plotCtrl | Plot internal controls of 450K or MethylationEPIC BeadChip.
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)
relic | RELIC dye bias correction method for Illumina HumanMethylation450 and MethylationEPIC BeadChip
rm.outlier | Filtering out outlier and/or low quality values