Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

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Documentation for package ‘ENmix’ version 1.24.0

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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"'