segmentSeq-package	segmentSeq-package
alignmentClass	alignmentClass-class
alignmentClass-class	alignmentClass-class
alignmentData	alignmentData-class
alignmentData-class	alignmentData-class
alignmentMeth	alignmentMeth-class
alignmentMeth-class	alignmentMeth-class
averageProfiles	averageMethylationRegions
c,lociData-method	lociData-class
cbind,alignmentClass-method	alignmentClass-class
cbind,alignmentData-method	alignmentData-class
cbind,alignmentMeth-method	alignmentMeth-class
classifySeg	classifySeg
dim,alignmentClass-method	alignmentClass-class
dim,alignmentData-method	alignmentData-class
dim,alignmentMeth-method	alignmentMeth-class
dim,lociData-method	lociData-class
dim,methData-method	methData-class
dim,segClass-method	segClass-class
dim,segData-method	segData-class
dim,segMeth-method	segMeth-class
findChunks	findChunks
getCounts	getCounts
getOverlaps	getOverlaps
givenExpression	givenExpression
heuristicSeg	heuristicSeg
hSL	hSL
initialize,alignmentClass-method	alignmentClass-class
initialize,alignmentData-method	alignmentData-class
initialize,alignmentMeth-method	alignmentMeth-class
initialize,segClass-method	segClass-class
initialize,segData-method	segData-class
initialize,segMeth-method	segMeth-class
lociData	lociData-class
lociData-class	lociData-class
lociLikelihoods	lociLikelihoods
mergeMethSegs	mergeMethSegs
methData	methData-class
methData-class	methData-class
normaliseNC	normaliseNC
plotAverageProfile	averageMethylationRegions
plotGenome	plotGenome
plotMeth	plotMeth
plotMethDistribution	plotMethDistribution
processAD	processAD
readBAM	readMethods
readGeneric	readMethods
readMeths	readMeths
segClass	segClass-class
segClass-class	segClass-class
segData	segData-class
segData-class	segData-class
segmentSeq	segmentSeq-package
segMeth	segMeth-class
segMeth-class	segMeth-class
selectLoci	selectLoci
show,alignmentClass-method	alignmentClass-class
show,alignmentData-method	alignmentData-class
show,alignmentMeth-method	alignmentMeth-class
show,lociData-method	lociData-class
show,methData-method	methData-class
show,segClass-method	segClass-class
show,segData-method	segData-class
show,segMeth-method	segMeth-class
SL10	SL
SL26	SL
SL32	SL
SL9	SL
summariseLoci	summariseLoci
thresholdFinder	thresholdFinder
[,alignmentClass,ANY,ANY,ANY-method	alignmentClass-class
[,alignmentClass,ANY,ANY-method	alignmentClass-class
[,alignmentClass,ANY-method	alignmentClass-class
[,alignmentClass-method	alignmentClass-class
[,alignmentData,ANY,ANY,ANY-method	alignmentData-class
[,alignmentData,ANY,ANY-method	alignmentData-class
[,alignmentData,ANY-method	alignmentData-class
[,alignmentData-method	alignmentData-class
[,alignmentMeth,ANY,ANY,ANY-method	alignmentMeth-class
[,alignmentMeth,ANY,ANY-method	alignmentMeth-class
[,alignmentMeth,ANY-method	alignmentMeth-class
[,alignmentMeth-method	alignmentMeth-class
[,lociData,ANY,ANY,ANY-method	lociData-class
[,lociData,ANY,ANY-method	lociData-class
[,lociData,ANY-method	lociData-class
[,lociData-method	lociData-class
[,methData,ANY,ANY,ANY-method	methData-class
[,methData,ANY,ANY-method	methData-class
[,methData,ANY-method	methData-class
[,methData-method	methData-class
[,segClass,ANY,ANY-method	segClass-class
[,segClass-method	segClass-class
[,segData,ANY,ANY-method	segData-class
[,segData,ANY-method	segData-class
[,segData-method	segData-class
[,segMeth,ANY,ANY-method	segMeth-class
[,segMeth,ANY-method	segMeth-class
[,segMeth-method	segMeth-class
