methylumi-package	methylumi-package
betas	generics
betas,GenomicMethylSet-method	methylumiGenerics
betas,MethylSet-method	methylumiGenerics
betas,MethyLumiM-method	MethyLumiM-class
betas,MethyLumiSet-method	MethyLumiSet-class
betas,RangedSummarizedExperiment-method	methylumiGenerics
betas<-	generics
betas<-,MethyLumiSet,matrix-method	MethyLumiSet-class
boxplot,MethyLumiSet-method	MethyLumiSet-class
combine,MethyLumiM,MethyLumiM-method	MethyLumiM-class
combine,MethyLumiQC,MethyLumiQC-method	MethyLumiQC-class
combine,MethyLumiSet,MethyLumiSet-method	MethyLumiSet-class
combine27k450k	methylumiGenerics
combine27k450k,MethyLumiSet,MethyLumiSet-method	MethyLumiSet-class
controlData	methylumiGenerics
controlData,MethyLumiM-method	MethyLumiM-class
controlData,MethyLumiSet-method	MethyLumiSet-class
controlData<-	methylumiGenerics
controlData<-,MethyLumiM,ANY-method	MethyLumiM-class
controlData<-,MethyLumiSet	MethyLumiSet-class
controlData<-,MethyLumiSet,MethyLumiQC-method	MethyLumiQC-class
controlTypes	qcplot
controlTypes,MethyLumiM-method	MethyLumiM-class
controlTypes,MethyLumiQC-method	MethyLumiQC-class
controlTypes,MethyLumiSet-method	MethyLumiSet-class
corplot	generics
corplot,MethyLumiSet-method	MethyLumiSet-class
CpGs	CpGs
cy3	methylumiGenerics
Cy3.N	methylumiGenerics
Cy3.N,MethyLumiQC-method	MethyLumiQC-class
Cy3.N,MethyLumiSet-method	MethyLumiSet-class
Cy3<-	methylumiGenerics
Cy3<-,MethyLumiQC,matrix-method	MethyLumiQC-class
cy5	methylumiGenerics
Cy5.N	methylumiGenerics
Cy5.N,MethyLumiQC-method	MethyLumiQC-class
Cy5.N,MethyLumiSet-method	MethyLumiSet-class
Cy5<-	methylumiGenerics
Cy5<-,MethyLumiQC,matrix-method	MethyLumiQC-class
dataType	methylumiGenerics
dataType,MethyLumiM-method	MethyLumiM-class
dataType<-	methylumiGenerics
dataType<-,MethyLumiM,ANY-method	MethyLumiM-class
dataType<-,MethyLumiM-method	MethyLumiM-class
designIItoMandU	methylumiGenerics
designItoMandU	methylumiGenerics
detection	methylumiGenerics
detection,MethyLumiM-method	MethyLumiM-class
detection<-	methylumiGenerics
detection<-,MethyLumiM-method	MethyLumiM-class
diagnostics	methylumiGenerics
diagnostics,methylData-method	methylData-class
estimateM	estimateM
exprs,MethyLumiSet-method	MethyLumiSet-class
extractBarcodeAndPosition	extractBarcodeAndPosition
featureFilter	featureFilter
featureFilter,MethyLumiM-method	featureFilter
featureFilter,MethyLumiSet-method	featureFilter
getAssayDataNameSubstitutions	getAssayDataNameSubstitutions
getBarcodes	methylumiGenerics
getHistory	generics
getHistory,MethyLumiM-method	MethyLumiM-class
getHistory,MethyLumiSet-method	MethyLumiSet-class
getProtocolData	methylumiGenerics
hist,MethyLumiQC-method	MethyLumiQC-class
hist,MethyLumiSet-method	MethyLumiSet-class
IDATsToDFs	methylumiGenerics
IDATsToMatrices	IDATsToMatrices
IDATtoDF	methylumiGenerics
IDATtoMatrix	IDATtoMatrix
intensities.IB	methylumiGenerics
intensities.IB,MethyLumiSet,character-method	MethyLumiSet-class
intensities.IB,MethyLumiSet,missing-method	MethyLumiSet-class
intensities.M	methylumiGenerics
intensities.M,MethyLumiSet,character-method	MethyLumiSet-class
intensities.M,MethyLumiSet,missing-method	MethyLumiSet-class
intensities.OOB	methylumiGenerics
intensities.OOB,MethyLumiSet,character-method	MethyLumiSet-class
intensities.OOB,MethyLumiSet,missing-method	MethyLumiSet-class
intensities.OOB.allelic	methylumiGenerics
intensities.OOB.allelic,MethyLumiSet,character,character-method	MethyLumiSet-class
intensities.OOB.allelic,MethyLumiSet,missing,missing-method	MethyLumiSet-class
intensities.U	methylumiGenerics
intensities.U,MethyLumiSet,character-method	MethyLumiSet-class
intensities.U,MethyLumiSet,missing-method	MethyLumiSet-class
intensitiesByChannel	methylumiGenerics
intensitiesByChannel,MethyLumiM-method	MethyLumiM-class
intensitiesByChannel,MethyLumiQC-method	MethyLumiQC-class
intensitiesByChannel,MethyLumiSet-method	MethyLumiSet-class
lumiCSV	methylumiGenerics
lumIDAT	methylumiGenerics
mergeProbeDesigns	methylumiGenerics
methylated	generics
methylated,MethylSet-method	methylumiGenerics
methylated,MethyLumi-method	MethyLumi-class
methylated,MethyLumiM-method	MethyLumiM-class
methylated,MethyLumiQC-method	MethyLumiQC-class
methylated,MethyLumiSet-method	MethyLumiSet-class
methylated.N	methylumiGenerics
methylated.N,methylData-method	methylData-class
methylated.N,MethyLumiM-method	MethyLumiM-class
methylated.N<-	methylumiGenerics
methylated.N<-,methylData,matrix-method	methylData-class
methylated.N<-,MethyLumiM,ANY-method	MethyLumiM-class
methylated<-	generics
methylated<-,MethyLumi,matrix-method	MethyLumi-class
methylated<-,MethyLumiM,ANY-method	MethyLumiM-class
methylated<-,MethyLumiSet,matrix-method	MethyLumiSet-class
methylData-class	methylData-class
methylumi	methylumi-package
MethyLumi-class	MethyLumi-class
methylumi.bgcorr	methylumiGenerics
methylumi.diagnostics	methylumiGenerics
methylumiCSV	methylumiGenerics
methylumIDAT	methylumIDAT
MethyLumiM	MethyLumiM-class
MethyLumiM-class	MethyLumiM-class
MethyLumiQC-class	MethyLumiQC-class
methylumiR	methylumiR
MethyLumiSet-class	MethyLumiSet-class
mldat	mldat
NChannelSetToMethyLumiSet	methylumiGenerics
negctls	methylumiGenerics
negctls,MethyLumiM,character-method	MethyLumiM-class
negctls,MethyLumiM,missing-method	MethyLumiM-class
negctls,MethyLumiQC,character-method	MethyLumiQC-class
negctls,MethyLumiQC,missing-method	MethyLumiQC-class
negctls,MethyLumiSet,character-method	MethyLumiSet-class
negctls,MethyLumiSet,missing-method	MethyLumiSet-class
negctls.stderr	methylumiGenerics
negctls.stderr,MethyLumiQC,character-method	MethyLumiQC-class
negctls.stderr,MethyLumiQC,missing-method	MethyLumiQC-class
negctls.stderr,MethyLumiSet,character-method	MethyLumiSet-class
negctls.stderr,MethyLumiSet,missing-method	MethyLumiSet-class
negnorm	methylumiGenerics
negnorm,MethyLumiM,character-method	MethyLumiM-class
negnorm,MethyLumiM,missing-method	MethyLumiM-class
negnorm,MethyLumiQC,character-method	MethyLumiQC-class
negnorm,MethyLumiQC,missing-method	MethyLumiQC-class
negnorm,MethyLumiSet,character-method	MethyLumiSet-class
negnorm,MethyLumiSet,missing-method	MethyLumiSet-class
normalizeMethyLumiSet	normalizeMethyLumiSet
normctls	methylumiGenerics
normctls,MethyLumiM-method	MethyLumiM-class
normctls,MethyLumiQC-method	MethyLumiQC-class
normctls,MethyLumiSet-method	MethyLumiSet-class
pairs,MethyLumiSet-method	MethyLumiSet-class
plotNAs	methylumiGenerics
plotNAs,methylData-method	methylData-class
plotNegOob	methylumiGenerics
plotSampleIntensities	plotSampleIntensities
plotSampleIntensities,MethyLumiSet-method	MethyLumiSet-class
probeNAs	methylumiGenerics
probeNAs,MethyLumiM-method	MethyLumiM-class
probeNAs,MethyLumiSet-method	MethyLumiSet-class
psummary	methylumiGenerics
pval.detect	methylumiGenerics
pval.detect,methylData-method	methylData-class
pval.detect<-	methylumiGenerics
pval.detect<-,methylData,numeric-method	methylData-class
pvals	generics
pvals,MethyLumi-method	MethyLumi-class
pvals,MethyLumiM-method	MethyLumiM-class
pvals<-	generics
pvals<-,MethyLumi,matrix-method	MethyLumi-class
qc.probe.plot	methylumiGenerics
QCdata	generics
QCdata,MethyLumiM-method	MethyLumiM-class
QCdata,MethyLumiSet-method	MethyLumiSet-class
QCdata<-	generics
QCdata<-,MethyLumiSet	MethyLumiSet-class
QCdata<-,MethyLumiSet,MethyLumiQC-method	MethyLumiQC-class
qcplot	qcplot
qcplot,Methylumi-method	MethyLumi-class
qcplot,MethyLumiQC-method	MethyLumiQC-class
qcplot,MethyLumiSet-method	MethyLumiSet-class
sampleNAs	methylumiGenerics
sampleNAs,MethyLumiM-method	MethyLumiM-class
sampleNAs,MethyLumiSet-method	MethyLumiSet-class
show,MethyLumiSet-method	MethyLumiSet-class
stripBeadNs	stripBeadExtras
stripBeadSDs	stripBeadExtras
stripMethyLumiSet	stripBeadExtras
stripOOB	stripBeadExtras
summary,MethyLumi-method	MethyLumi-class
tcgaPipeline	tcgaPipeline
total.intensity	methylumiGenerics
total.intensity,MethyLumiM-method	MethyLumiM-class
total.intensity,MethyLumiSet-method	MethyLumiSet-class
unmethylated	generics
unmethylated,MethylSet-method	methylumiGenerics
unmethylated,MethyLumi-method	MethyLumi-class
unmethylated,MethyLumiM-method	MethyLumiM-class
unmethylated,MethyLumiQC-method	MethyLumiQC-class
unmethylated,MethyLumiSet-method	MethyLumiSet-class
unmethylated.N	methylumiGenerics
unmethylated.N,methylData-method	methylData-class
unmethylated.N,MethyLumiM-method	MethyLumiM-class
unmethylated.N<-	methylumiGenerics
unmethylated.N<-,methylData,matrix-method	methylData-class
unmethylated.N<-,MethyLumiM,ANY-method	MethyLumiM-class
unmethylated<-	generics
unmethylated<-,MethyLumi,matrix-method	MethyLumi-class
unmethylated<-,MethyLumiM,ANY-method	MethyLumiM-class
unmethylated<-,MethyLumiSet,matrix-method	MethyLumiSet-class
varFilter	varFilter
varFilter,MethyLumiM-method	varFilter
varFilter,MethyLumiSet-method	varFilter
[,MethyLumiM,ANY,ANY,ANY-method	MethyLumiM-class
[,MethyLumiM,ANY-method	MethyLumiM-class
[,MethyLumiSet,ANY,ANY,ANY-method	MethyLumiSet-class
[,MethyLumiSet,ANY-method	MethyLumiSet-class
