# Handle Illumina methylation data

## Documentation for package ‘methylumi’ version 2.57.0

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

## Help Pages

B C D E F G H I L M N P Q S T U V misc

methylumi-package | Handle Illumina methylation data

## -- B --

betas | methylumi accessors
betas-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
betas-method | Class '"MethyLumiSet"' for containing Illumina methylation data
betas-method | Generics defined in methylumi
betas<- | methylumi accessors
betas<--method | Class '"MethyLumiSet"' for containing Illumina methylation data
boxplot-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- C --

combine-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
combine-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
combine-method | Class '"MethyLumiSet"' for containing Illumina methylation data
combine27k450k | Generics defined in methylumi
combine27k450k-method | Class '"MethyLumiSet"' for containing Illumina methylation data
controlData | Generics defined in methylumi
controlData-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlData-method | Class '"MethyLumiSet"' for containing Illumina methylation data
controlData<- | Generics defined in methylumi
controlData<-,MethyLumiSet | Class '"MethyLumiSet"' for containing Illumina methylation data
controlData<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlData<--method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
controlTypes | Methods for dealing with control data for Illumina methylation data.
controlTypes-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlTypes-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
controlTypes-method | Class '"MethyLumiSet"' for containing Illumina methylation data
corplot | methylumi accessors
corplot-method | Class '"MethyLumiSet"' for containing Illumina methylation data
CpGs | Data frame describing loci on the 27 and 450k arrays.
cy3 | Generics defined in methylumi
Cy3.N | Generics defined in methylumi
Cy3.N-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
Cy3.N-method | Class '"MethyLumiSet"' for containing Illumina methylation data
Cy3<- | Generics defined in methylumi
Cy3<--method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
cy5 | Generics defined in methylumi
Cy5.N | Generics defined in methylumi
Cy5.N-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
Cy5.N-method | Class '"MethyLumiSet"' for containing Illumina methylation data
Cy5<- | Generics defined in methylumi
Cy5<--method | Class '"MethyLumiQC"' for holding Illumina methylation QC data

## -- D --

dataType | Generics defined in methylumi
dataType-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
dataType<- | Generics defined in methylumi
dataType<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
designIItoMandU | Generics defined in methylumi
designItoMandU | Generics defined in methylumi
detection | Generics defined in methylumi
detection-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
detection<- | Generics defined in methylumi
detection<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
diagnostics | Generics defined in methylumi
diagnostics-method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM

## -- E --

estimateM | Estimate methylation M-value matrix
exprs-method | Class '"MethyLumiSet"' for containing Illumina methylation data
extractBarcodeAndPosition | Extract the Barcode and Position Information from Sentrix ID

## -- F --

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

## -- G --

getAssayDataNameSubstitutions | Return a data.frame of AssayData name substitutions.
getBarcodes | Generics defined in methylumi
getHistory | methylumi accessors
getHistory-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
getHistory-method | Class '"MethyLumiSet"' for containing Illumina methylation data
getProtocolData | Generics defined in methylumi

## -- H --

hist-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
hist-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- I --

IDATsToDFs | Generics defined in methylumi
IDATsToMatrices | convert multiple idats to matrices
IDATtoDF | Generics defined in methylumi
IDATtoMatrix | process a single IDAT (just the mean intensities)
intensities.IB | Generics defined in methylumi
intensities.IB-method | Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.M | Generics defined in methylumi
intensities.M-method | Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.OOB | Generics defined in methylumi
intensities.OOB-method | Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.OOB.allelic | Generics defined in methylumi
intensities.OOB.allelic-method | Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.U | Generics defined in methylumi
intensities.U-method | Class '"MethyLumiSet"' for containing Illumina methylation data
intensitiesByChannel | Generics defined in methylumi
intensitiesByChannel-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
intensitiesByChannel-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
intensitiesByChannel-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- L --

lumiCSV | Generics defined in methylumi
lumIDAT | Generics defined in methylumi

## -- M --

mergeProbeDesigns | Generics defined in methylumi
methylated | methylumi accessors
methylated-method | The base class for storing Illumina Methylation data
methylated-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
methylated-method | Class '"MethyLumiSet"' for containing Illumina methylation data
methylated-method | Generics defined in methylumi
methylated.N | Generics defined in methylumi
methylated.N-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated.N-method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylated.N<- | Generics defined in methylumi
methylated.N<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated.N<--method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylated<- | methylumi accessors
methylated<--method | The base class for storing Illumina Methylation data
methylated<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated<--method | Class '"MethyLumiSet"' for containing Illumina methylation data
methylData-class | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylumi | Handle Illumina methylation data
MethyLumi-class | The base class for storing Illumina Methylation data
methylumi.bgcorr | Generics defined in methylumi
methylumi.diagnostics | Generics defined in methylumi
methylumiCSV | Generics defined in methylumi
methylumIDAT | methylumIDAT
MethyLumiM | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
MethyLumiM-class | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
MethyLumiQC-class | Class '"MethyLumiQC"' for holding Illumina methylation QC data
methylumiR | Load data from Illumina methylation platform
MethyLumiSet-class | Class '"MethyLumiSet"' for containing Illumina methylation data
mldat | Example SAM format Illumina methylation dataset

## -- N --

NChannelSetToMethyLumiSet | Generics defined in methylumi
negctls | Generics defined in methylumi
negctls-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
negctls-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
negctls-method | Class '"MethyLumiSet"' for containing Illumina methylation data
negctls.stderr | Generics defined in methylumi
negctls.stderr-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
negctls.stderr-method | Class '"MethyLumiSet"' for containing Illumina methylation data
negnorm | Generics defined in methylumi
negnorm-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
negnorm-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
negnorm-method | Class '"MethyLumiSet"' for containing Illumina methylation data
normalizeMethyLumiSet | Normalize a MethyLumiSet, accounting for dye bias
normctls | Generics defined in methylumi
normctls-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
normctls-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
normctls-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- P --

pairs-method | Class '"MethyLumiSet"' for containing Illumina methylation data
plotNAs | Generics defined in methylumi
plotNAs-method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
plotNegOob | Generics defined in methylumi
plotSampleIntensities | Plot the sample intensities.
plotSampleIntensities-method | Class '"MethyLumiSet"' for containing Illumina methylation data
probeNAs | Generics defined in methylumi
probeNAs-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
probeNAs-method | Class '"MethyLumiSet"' for containing Illumina methylation data
psummary | Generics defined in methylumi
pval.detect | Generics defined in methylumi
pval.detect-method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
pval.detect<- | Generics defined in methylumi
pval.detect<--method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
pvals | methylumi accessors
pvals-method | The base class for storing Illumina Methylation data
pvals-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
pvals<- | methylumi accessors
pvals<--method | The base class for storing Illumina Methylation data

## -- Q --

qc.probe.plot | Generics defined in methylumi
QCdata | methylumi accessors
QCdata-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
QCdata-method | Class '"MethyLumiSet"' for containing Illumina methylation data
QCdata<- | methylumi accessors
QCdata<-,MethyLumiSet | Class '"MethyLumiSet"' for containing Illumina methylation data
QCdata<--method | Class '"MethyLumiQC"' for holding 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 '"MethyLumiQC"' for holding Illumina methylation QC data
qcplot-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- S --

sampleNAs | Generics defined in methylumi
sampleNAs-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
sampleNAs-method | Class '"MethyLumiSet"' for containing Illumina methylation data
show-method | Class '"MethyLumiSet"' for containing Illumina methylation data
stripBeadNs | Strip excessive probe-level data from MethyLumiSets
stripBeadSDs | Strip excessive probe-level data from MethyLumiSets
stripMethyLumiSet | Strip excessive probe-level data from MethyLumiSets
stripOOB | Strip excessive probe-level data from MethyLumiSets
summary-method | The base class for storing Illumina Methylation data

## -- T --

tcgaPipeline | Total convenience function for processing IDATs like tcga
total.intensity | Generics defined in methylumi
total.intensity-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
total.intensity-method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- U --

unmethylated | methylumi accessors
unmethylated-method | The base class for storing Illumina Methylation data
unmethylated-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data
unmethylated-method | Class '"MethyLumiSet"' for containing Illumina methylation data
unmethylated-method | Generics defined in methylumi
unmethylated.N | Generics defined in methylumi
unmethylated.N-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated.N-method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
unmethylated.N<- | Generics defined in methylumi
unmethylated.N<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated.N<--method | Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
unmethylated<- | methylumi accessors
unmethylated<--method | The base class for storing Illumina Methylation data
unmethylated<--method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated<--method | Class '"MethyLumiSet"' for containing Illumina methylation data

## -- V --

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

## -- misc --

[-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
[-method | Class '"MethyLumiSet"' for containing Illumina methylation data