minfi-package	minfi-package
addQC	getQC
addSex	getSex
addSnpInfo	getAnnotation
annotation,GenomicMethylSet-method	GenomicMethylSet-class
annotation,GenomicRatioSet-method	GenomicRatioSet-class
annotation,MethylSet-method	MethylSet-class
annotation,RatioSet-method	RatioSet-class
annotation,RGChannelSet-method	RGChannelSet-class
annotation<-,GenomicMethylSet,ANY-method	GenomicMethylSet-class
annotation<-,GenomicRatioSet,ANY-method	GenomicRatioSet-class
annotation<-,MethylSet,ANY-method	MethylSet-class
annotation<-,RatioSet,ANY-method	RatioSet-class
annotation<-,RGChannelSet,ANY-method	RGChannelSet-class
bgcorrect.illumina	preprocessIllumina
blockFinder	blockFinder
bumphunter,GenomicRatioSet-method	bumphunter
coerce,RGChannelSetExtended,RGChannelSet-method	RGChannelSet-class
combine,GenomicMethylSet,GenomicMethylSet-method	GenomicMethylSet-class
combine,GenomicRatioSet,GenomicRatioSet-method	GenomicRatioSet-class
combine,MethylSet,MethylSet-method	MethylSet-class
combine,RatioSet,RatioSet-method	RatioSet-class
combine,RGChannelSet,RGChannelSet-method	RGChannelSet-class
combineArrays	combineArrays
combineArrays,GenomicMethylSet,GenomicMethylSet-method	combineArrays
combineArrays,GenomicRatioSet,GenomicRatioSet-method	combineArrays
combineArrays,MethylSet,MethylSet-method	combineArrays
combineArrays,RatioSet,RatioSet-method	combineArrays
combineArrays,RGChannelSet,RGChannelSet-method	combineArrays
compartments	compartments
controlStripPlot	controlStripPlot
convertArray	convertArray
convertArray,GenomicMethylSet-method	convertArray
convertArray,GenomicRatioSet-method	convertArray
convertArray,MethylSet-method	convertArray
convertArray,RatioSet-method	convertArray
convertArray,RGChannelSet-method	convertArray
cpgCollapse	cpgCollapse
createCorMatrix	compartments
densityBeanPlot	densityBeanPlot
densityPlot	densityPlot
detectionP	detectionP
dimnames,arrayRealizationSink-method	DelayedArray_utils
dmpFinder	dmpFinder
dropLociWithSnps	getAnnotation
dropMethylationLoci	MethylSet-class
estimateCellCounts	estimateCellCounts
extractAB	compartments
featureNames,GenomicMethylSet-method	GenomicMethylSet-class
featureNames,GenomicRatioSet-method	GenomicRatioSet-class
featureNames,MethylSet-method	MethylSet-class
featureNames,RatioSet-method	RatioSet-class
featureNames,RGChannelSet-method	RGChannelSet-class
featureNames<-,GenomicMethylSet-method	GenomicMethylSet-class
featureNames<-,GenomicRatioSet-method	GenomicRatioSet-class
featureNames<-,MethylSet-method	MethylSet-class
featureNames<-,RatioSet-method	RatioSet-class
featureNames<-,RGChannelSet-method	RGChannelSet-class
fixMethOutliers	fixMethOutliers
gaphunter	gaphunter
GenomicMethylSet	GenomicMethylSet-class
GenomicMethylSet-class	GenomicMethylSet-class
GenomicRatioSet	GenomicRatioSet-class
GenomicRatioSet-class	GenomicRatioSet-class
getAnnotation	getAnnotation
getAnnotationObject	getAnnotation
getBeta	MethylSet-class
getBeta,GenomicMethylSet-method	GenomicMethylSet-class
getBeta,GenomicRatioSet-method	GenomicRatioSet-class
getBeta,MethylSet-method	MethylSet-class
getBeta,RatioSet-method	RatioSet-class
getBeta,RGChannelSet-method	RGChannelSet-class
getCN	GenomicRatioSet-class
getCN,GenomicMethylSet-method	GenomicMethylSet-class
getCN,GenomicRatioSet-method	GenomicRatioSet-class
getCN,MethylSet-method	MethylSet-class
getCN,RatioSet-method	RatioSet-class
getControlAddress	IlluminaMethylationManifest-class
getGenomicRatioSetFromGEO	getGenomicRatioSetFromGEO
getGreen	RGChannelSet-class
getIslandStatus	getAnnotation
getLocations	getAnnotation
getM	MethylSet-class
getM,GenomicMethylSet-method	GenomicMethylSet-class
getM,GenomicRatioSet-method	GenomicRatioSet-class
getM,MethylSet-method	MethylSet-class
getM,RatioSet-method	RatioSet-class
getManifest	IlluminaMethylationManifest-class
getManifest,character-method	IlluminaMethylationManifest-class
getManifest,IlluminaMethylationAnnotation-method	IlluminaMethylationAnnotation-class
getManifest,IlluminaMethylationManifest-method	IlluminaMethylationManifest-class
getManifest,MethylSet-method	MethylSet-class
getManifest,RGChannelSet-method	RGChannelSet-class
getManifestInfo	IlluminaMethylationManifest-class
getMeth	MethylSet-class
getMeth,GenomicMethylSet-method	GenomicMethylSet-class
getMeth,MethylSet-method	MethylSet-class
getMethSignal	utils
getNBeads	RGChannelSet-class
getOOB	RGChannelSet-class
getProbeInfo	IlluminaMethylationManifest-class
getProbeType	getAnnotation
getQC	getQC
getRed	RGChannelSet-class
getSex	getSex
getSnpBeta	RGChannelSet-class
getSnpInfo	getAnnotation
getUnmeth	MethylSet-class
getUnmeth,GenomicMethylSet-method	GenomicMethylSet-class
getUnmeth,MethylSet-method	MethylSet-class
IlluminaMethylationAnnotation	IlluminaMethylationAnnotation-class
IlluminaMethylationAnnotation-class	IlluminaMethylationAnnotation-class
IlluminaMethylationManifest	IlluminaMethylationManifest-class
IlluminaMethylationManifest-class	IlluminaMethylationManifest-class
ilogit2	logit2
logit2	logit2
makeGenomicRatioSetFromMatrix	makeGenomicRatioSetFromMatrix
mapToGenome	mapToGenome-methods
mapToGenome,GenomicMethylSet-method	GenomicMethylSet-class
mapToGenome,GenomicRatioSet-method	GenomicRatioSet-class
mapToGenome,MethylSet-method	mapToGenome-methods
mapToGenome,RatioSet-method	mapToGenome-methods
mapToGenome,RGChannelSet-method	mapToGenome-methods
mapToGenome-methods	mapToGenome-methods
mdsPlot	mdsPlot
MethylSet	MethylSet-class
MethylSet-class	MethylSet-class
minfi	minfi-package
minfi-defunct	minfi-defunct
minfi-deprecated	minfi-deprecated
minfiQC	minfiQC
normalize.illumina.control	preprocessIllumina
pData,GenomicMethylSet-method	GenomicMethylSet-class
pData,GenomicRatioSet-method	GenomicRatioSet-class
pData,MethylSet-method	MethylSet-class
pData,RatioSet-method	RatioSet-class
pData,RGChannelSet-method	RGChannelSet-class
pData<-,GenomicMethylSet,DataFrame-method	GenomicMethylSet-class
pData<-,GenomicRatioSet,DataFrame-method	GenomicRatioSet-class
pData<-,MethylSet,DataFrame-method	MethylSet-class
pData<-,RatioSet,DataFrame-method	RatioSet-class
pData<-,RGChannelSet,DataFrame-method	RGChannelSet-class
plotBetasByType	plotBetasByType
plotCpg	plotCpg
plotQC	getQC
plotSex	getSex
preprocessFunnorm	preprocessFunnorm
preprocessIllumina	preprocessIllumina
preprocessMethod	MethylSet-class
preprocessMethod,GenomicMethylSet-method	GenomicMethylSet-class
preprocessMethod,GenomicRatioSet-method	GenomicRatioSet-class
preprocessMethod,MethylSet-method	MethylSet-class
preprocessMethod,RatioSet-method	RatioSet-class
preprocessNoob	preprocessNoob
preprocessQuantile	preprocessQuantile
preprocessRaw	preprocessRaw
preprocessSWAN	preprocessSwan
qcReport	qcReport
ratioConvert	ratioConvert-methods
ratioConvert,GenomicMethylSet-method	ratioConvert-methods
ratioConvert,MethylSet-method	ratioConvert-methods
ratioConvert-methods	ratioConvert-methods
RatioSet	RatioSet-class
RatioSet-class	RatioSet-class
read.450k	minfi-defunct
read.450k.exp	minfi-defunct
read.450k.sheet	minfi-defunct
read.metharray	read.metharray
read.metharray.exp	read.metharray.exp
read.metharray.sheet	read.metharray.sheet
readGEORawFile	readGEORawFile
readTCGA	readTCGA
RGChannelSet	RGChannelSet-class
RGChannelSet-class	RGChannelSet-class
RGChannelSetExtended	RGChannelSet-class
RGChannelSetExtended-class	RGChannelSet-class
sampleNames,GenomicMethylSet-method	GenomicMethylSet-class
sampleNames,GenomicRatioSet-method	GenomicRatioSet-class
sampleNames,MethylSet-method	MethylSet-class
sampleNames,RatioSet-method	RatioSet-class
sampleNames,RGChannelSet-method	RGChannelSet-class
sampleNames<-,GenomicMethylSet,ANY-method	GenomicMethylSet-class
sampleNames<-,GenomicRatioSet,ANY-method	GenomicRatioSet-class
sampleNames<-,MethylSet,ANY-method	MethylSet-class
sampleNames<-,RatioSet,ANY-method	RatioSet-class
sampleNames<-,RGChannelSet,ANY-method	RGChannelSet-class
show,GenomicMethylSet-method	GenomicMethylSet-class
show,GenomicRatioSet-method	GenomicRatioSet-class
show,IlluminaMethylationAnnotation-method	IlluminaMethylationAnnotation-class
show,IlluminaMethylationManifest-method	IlluminaMethylationManifest-class
show,MethylSet-method	MethylSet-class
show,RatioSet-method	RatioSet-class
show,RGChannelSet-method	RGChannelSet-class
subsetByLoci	subsetByLoci
type,arrayRealizationSink-method	DelayedArray_utils
type,HDF5RealizationSink-method	DelayedArray_utils
type,RleRealizationSink-method	DelayedArray_utils
