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

## Documentation for package ‘ENmix’ version 1.24.0

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

## Help Pages

B2M | Convert Beta value to M value.
calc_detP | Calculate detection P values
combp | Differentially methylated region finder using a modified comb-p method
ctrlsva | Non-negative control surrogate variables
dupicc | Methylation duplicates evaluation.
estimateCellProp | Cell Proportion Estimation
freqpoly | Frequency polygon plot
getB | Extract Beta value.
getCGinfo | CpG probe annotation inforamtion
getmeth | Create a methDataSet
ipdmr | Differentially methylated region finder using interval P values
M2B | Convert M value to Beta value.
methDataSet | Class '"methDataSet"'
methDataSet-class | Class '"methDataSet"'
methyAge | Calculate Methylation Age
mhtplot | P value manhattan plot
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.
p.qqplot | P value Q-Q plot
pcrplot | Principal component regression plot
plotCtrl | Plot internal controls of 450K or MethylationEPIC BeadChip.
predSex | Estimating sample sex based on methylation data
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"'