# Handle Illumina methylation data

## Documentation for package ‘methylumi’ version 1.0.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

methylumi-package | Handle Illumina methylation data
betas | methylumi accessors
betas,MethyLumiSet-method | Class to hold Illumina Methylation data
betas<- | methylumi accessors
betas<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data
boxplot,MethyLumiSet-method | Class to hold Illumina Methylation data
combine,MethyLumiSet,MethyLumiSet-method | Class to hold Illumina Methylation data
controlTypes | Methods for dealing with control data for Illumina methylation data.
controlTypes,MethyLumiQC-method | Class to hold Illumina Methylation QC data
controlTypes,MethyLumiSet-method | Class to hold Illumina Methylation data
corplot,MethyLumiSet-method | Class to hold Illumina Methylation data
exprs,MethyLumiQC-method | Class to hold Illumina Methylation QC data
exprs,MethyLumiSet-method | Class to hold Illumina Methylation data
exprs<-,MethyLumiQC,matrix-method | Class to hold Illumina Methylation QC data
exprs<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data
extractBarcodeAndPosition | Extract the Barcode and Position Information from Sentrix ID
getAssayDataNameSubstitutions | Return a data.frame of AssayData name substitutions.
getHistory | methylumi accessors
getHistory,MethyLumiSet-method | Class to hold Illumina Methylation data
hist,MethyLumiSet-method | Class to hold Illumina Methylation data
initialize,MethyLumiQC-method | Class to hold Illumina Methylation QC data
initialize,MethyLumiSet-method | Class to hold Illumina Methylation data
methylated | methylumi accessors
methylated,MethyLumi-method | The base class for storing Illumina Methylation data
methylated,MethyLumiSet-method | Class to hold Illumina Methylation data
methylated<- | methylumi accessors
methylated<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data
methylated<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data
methylumi | Handle Illumina methylation data
MethyLumi-class | The base class for storing Illumina Methylation data
MethyLumiQC-class | Class to hold Illumina Methylation QC data
methylumiR | Load data from Illumina methylation platform
MethyLumiSet-class | Class to hold Illumina Methylation data
mldat | Example SAM format Illumina methylation dataset
normalizeMethyLumiSet | Normalize a MethyLumiSet, accounting for dye bias
pairs,MethyLumiSet-method | Class to hold Illumina Methylation data
plotSampleIntensities | Plot the sample intensities.
plotSampleIntensities,MethyLumiSet-method | Class to hold Illumina Methylation data
pvals | methylumi accessors
pvals,MethyLumi-method | The base class for storing Illumina Methylation data
pvals<- | methylumi accessors
pvals<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data
QCdata | methylumi accessors
QCdata,MethyLumiSet-method | Class to hold Illumina Methylation data
QCdata<- | methylumi accessors
QCdata<-,MethyLumiSet,MethyLumiQC-method | Class to hold Illumina Methylation data
QCDataOrNULL-class | Class to hold Illumina Methylation QC data
qcplot | Methods for dealing with control data for Illumina methylation data.
qcplot,Methylumi-method | The base class for storing Illumina Methylation data
qcplot,MethyLumiQC-method | Class to hold Illumina Methylation QC data
qcplot,MethyLumiSet-method | Class to hold Illumina Methylation data
show,MethyLumiSet-method | Class to hold Illumina Methylation data
summary,MethyLumi-method | The base class for storing Illumina Methylation data
unmethylated | methylumi accessors
unmethylated,MethyLumi-method | The base class for storing Illumina Methylation data
unmethylated,MethyLumiSet-method | Class to hold Illumina Methylation data
unmethylated<- | methylumi accessors
unmethylated<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data
unmethylated<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data
[,MethyLumiSet-method | Class to hold Illumina Methylation data