Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip


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Documentation for package ‘ENmix’ version 1.12.4

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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