minfi-package	minfi-package
annotation,GenomicMethylSet-method	GenomicMethylSet-class
bgcorrect.illumina	preprocessIllumina
controlStripPlot	controlStripPlot
densityBeanPlot	densityBeanPlot
densityPlot	densityPlot
detectionP	detectionP
dmpFinder	dmpFinder
dropMethylationLoci	MethylSet-class
featureNames,GenomicMethylSet-method	GenomicMethylSet-class
GenomicMethylSet	GenomicMethylSet-class
GenomicMethylSet-class	GenomicMethylSet-class
getBeta	MethylSet-class
getBeta,GenomicMethylSet-method	GenomicMethylSet-class
getBeta,MethylSet-method	MethylSet-class
getBeta,RGChannelSet-method	RGChannelSet-class
getControlAddress	IlluminaMethylationManifest-class
getControlTypes	IlluminaMethylationManifest-class
getGreen	RGChannelSet-class
getLocations	IlluminaMethylationAnnotation-class
getLocations,IlluminaMethylationAnnotation-method	IlluminaMethylationAnnotation-class
getLocations,MethylSet-method	MethylSet-class
getM	MethylSet-class
getM,GenomicMethylSet-method	GenomicMethylSet-class
getM,MethylSet-method	MethylSet-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
getProbeInfo	IlluminaMethylationManifest-class
getRed	RGChannelSet-class
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
initialize,MethylSet-method	MethylSet-class
initialize,RGChannelSet-method	RGChannelSet-class
initialize,RGChannelSetExtended-method	RGChannelSet-class
logit2	logit2
mapToGenome	mapToGenome-methods
mapToGenome,MethylSet-method	mapToGenome-methods
mapToGenome,RGChannelSet-method	mapToGenome-methods
mapToGenome-methods	mapToGenome-methods
mdsPlot	mdsPlot
MethylSet	MethylSet-class
MethylSet-class	MethylSet-class
minfi	minfi-package
normalize.illumina.control	preprocessIllumina
pData,GenomicMethylSet-method	GenomicMethylSet-class
plotBetasByType	plotBetasByType
plotCpg	plotCpg
preprocessIllumina	preprocessIllumina
preprocessMethod	MethylSet-class
preprocessMethod,GenomicMethylSet-method	GenomicMethylSet-class
preprocessMethod,MethylSet-method	MethylSet-class
preprocessRaw	preprocessRaw
preprocessSWAN	preprocessSwan
qcReport	qcReport
read.450k	read.450k
read.450k.exp	read.450k.exp
read.450k.sheet	read.450k.sheet
RGChannelSet	RGChannelSet-class
RGChannelSet-class	RGChannelSet-class
RGChannelSetExtended	RGChannelSet-class
RGChannelSetExtended-class	RGChannelSet-class
sampleNames,GenomicMethylSet-method	GenomicMethylSet-class
show,GenomicMethylSet-method	GenomicMethylSet-class
show,IlluminaMethylationAnnotation-method	IlluminaMethylationAnnotation-class
show,IlluminaMethylationManifest-method	IlluminaMethylationManifest-class
show,MethylSet-method	MethylSet-class
show,RGChannelSet-method	RGChannelSet-class
