# Handle Illumina methylation data

## Documentation for package ‘methylumi’ version 1.8.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

methylumi-package | Handle Illumina methylation data
betas | methylumi accessors
betas-method | Class to hold Illumina Methylation data
betas<- | methylumi accessors
betas<--method | Class to hold Illumina Methylation data
boxplot-method | Class to hold Illumina Methylation data
coerce-method | Class "MethyLumiM": for Illumina Methylation microarray data
combine-method | Class "MethyLumiM": for Illumina Methylation microarray data
combine-method | Class to hold Illumina Methylation data
controlData | Class "MethyLumiM": for Illumina Methylation microarray data
controlData-method | Class "MethyLumiM": for Illumina Methylation microarray data
controlData<- | Class "MethyLumiM": for Illumina Methylation microarray data
controlData<--method | Class "MethyLumiM": for Illumina Methylation microarray data
controlTypes | Methods for dealing with control data for Illumina methylation data.
controlTypes-method | Class to hold Illumina Methylation QC data
controlTypes-method | Class to hold Illumina Methylation data
corplot | methylumi accessors
corplot-method | Class to hold Illumina Methylation data
detection | Class "MethyLumiM": for Illumina Methylation microarray data
detection-method | Class "MethyLumiM": for Illumina Methylation microarray data
detection<- | Class "MethyLumiM": for Illumina Methylation microarray data
detection<--method | Class "MethyLumiM": for Illumina Methylation microarray data
estimateM | Estimate methylation M-value matrix
exprs-method | Class to hold Illumina Methylation QC data
exprs-method | Class to hold Illumina Methylation data
exprs<--method | Class to hold Illumina Methylation QC data
exprs<--method | Class to hold Illumina Methylation data
extractBarcodeAndPosition | Extract the Barcode and Position Information from Sentrix ID
featureFilter | Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
featureFilter-method | Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
getAssayDataNameSubstitutions | Return a data.frame of AssayData name substitutions.
getHistory | methylumi accessors
getHistory-method | Class "MethyLumiM": for Illumina Methylation microarray data
getHistory-method | Class to hold Illumina Methylation data
hist-method | Class to hold Illumina Methylation data
initialize-method | Class "MethyLumiM": for Illumina Methylation microarray data
initialize-method | Class to hold Illumina Methylation QC data
initialize-method | Class to hold Illumina Methylation data
methylated | methylumi accessors
methylated-method | The base class for storing Illumina Methylation data
methylated-method | Class "MethyLumiM": for Illumina Methylation microarray data
methylated-method | Class to hold Illumina Methylation data
methylated.N | Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N-method | Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N<- | Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N<--method | Class "MethyLumiM": for Illumina Methylation microarray data
methylated<- | methylumi accessors
methylated<--method | The base class for storing Illumina Methylation data
methylated<--method | Class "MethyLumiM": for Illumina Methylation microarray data
methylated<--method | Class to hold Illumina Methylation data
methylumi | Handle Illumina methylation data
MethyLumi-class | The base class for storing Illumina Methylation data
MethyLumiM-class | Class "MethyLumiM": for Illumina Methylation microarray 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-method | Class to hold Illumina Methylation data
plotSampleIntensities | Plot the sample intensities.
plotSampleIntensities-method | Class to hold Illumina Methylation data
pvals | methylumi accessors
pvals-method | The base class for storing Illumina Methylation data
pvals<- | methylumi accessors
pvals<--method | The base class for storing Illumina Methylation data
QCdata | methylumi accessors
QCdata-method | Class to hold Illumina Methylation data
QCdata<- | methylumi accessors
QCdata<--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-method | The base class for storing Illumina Methylation data
qcplot-method | Class to hold Illumina Methylation QC data
qcplot-method | Class to hold Illumina Methylation data
show-method | Class to hold Illumina Methylation data
summary-method | The base class for storing Illumina Methylation data
unmethylated | methylumi accessors
unmethylated-method | The base class for storing Illumina Methylation data
unmethylated-method | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated-method | Class to hold Illumina Methylation data
unmethylated.N | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N-method | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N<- | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N<--method | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated<- | methylumi accessors
unmethylated<--method | The base class for storing Illumina Methylation data
unmethylated<--method | Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated<--method | Class to hold Illumina Methylation data
varFilter | Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
varFilter-method | Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
[-method | Class "MethyLumiM": for Illumina Methylation microarray data
[-method | Class to hold Illumina Methylation data