adjust.methylC	methylKit-defunct
adjustMethylC	adjustMethylC
adjustMethylC,methylRaw,methylRaw-method	adjustMethylC
adjustMethylC,methylRawDB,methylRawDB-method	adjustMethylC
adjustMethylC,methylRawList,methylRawList-method	adjustMethylC
adjustMethylC,methylRawListDB,methylRawListDB-method	adjustMethylC
annotate.WithFeature	methylKit-defunct
annotate.WithFeature.Flank	methylKit-defunct
annotate.WithGenicParts	methylKit-defunct
assocComp	assocComp-methods
bedgraph	bedgraph-methods
bedgraph,methylDiff-method	bedgraph-methods
bedgraph,methylDiffDB-method	bedgraph-methods
bedgraph,methylRaw-method	bedgraph-methods
bedgraph,methylRawDB-method	bedgraph-methods
bedgraph,methylRawList-method	bedgraph-methods
bedgraph,methylRawListDB-method	bedgraph-methods
calculateDiffMeth	calculateDiffMeth-methods
calculateDiffMeth,methylBase-method	calculateDiffMeth-methods
calculateDiffMeth,methylBaseDB-method	calculateDiffMeth-methods
calculateDiffMethDSS	calculateDiffMethDSS-methods
calculateDiffMethDSS,methylBase-method	calculateDiffMethDSS-methods
clusterSamples	clusterSamples-methods
clusterSamples,methylBase-method	clusterSamples-methods
clusterSamples,methylBaseDB-method	clusterSamples-methods
dataSim	dataSim-methods
diffMethPerChr	diffMethPerChr-methods
diffMethPerChr,methylDiff-method	diffMethPerChr-methods
diffMethPerChr,methylDiffDB-method	diffMethPerChr-methods
extract	extract-methods
extract,methylBase,ANY-method	extract-methods
extract,methylBaseDB,ANY-method	extract-methods
extract,methylDiff,ANY-method	extract-methods
extract,methylDiffDB,ANY-method	extract-methods
extract,methylRaw,ANY-method	extract-methods
extract,methylRawDB,ANY-method	extract-methods
filterByCoverage	filterByCoverage-methods
filterByCoverage,methylRaw-method	filterByCoverage-methods
filterByCoverage,methylRawDB-method	filterByCoverage-methods
filterByCoverage,methylRawList-method	filterByCoverage-methods
filterByCoverage,methylRawListDB-method	filterByCoverage-methods
get.methylDiff	methylKit-defunct
getAssembly	getAssembly-methods
getAssembly,methylBase-method	getAssembly-methods
getAssembly,methylBaseDB-method	getAssembly-methods
getAssembly,methylDiff-method	getAssembly-methods
getAssembly,methylDiffDB-method	getAssembly-methods
getAssembly,methylRaw-method	getAssembly-methods
getAssembly,methylRawDB-method	getAssembly-methods
getContext	getContext-methods
getContext,methylBase-method	getContext-methods
getContext,methylBaseDB-method	getContext-methods
getContext,methylDiff-method	getContext-methods
getContext,methylDiffDB-method	getContext-methods
getContext,methylRaw-method	getContext-methods
getContext,methylRawDB-method	getContext-methods
getCorrelation	getCorrelation-methods
getCorrelation,methylBase-method	getCorrelation-methods
getCorrelation,methylBaseDB-method	getCorrelation-methods
getCoverageStats	getCoverageStats-methods
getCoverageStats,methylRaw-method	getCoverageStats-methods
getCoverageStats,methylRawDB-method	getCoverageStats-methods
getData	getData-methods
getData,methylBase-method	getData-methods
getData,methylBaseDB-method	getData-methods
getData,methylDiff-method	getData-methods
getData,methylDiffDB-method	getData-methods
getData,methylRaw-method	getData-methods
getData,methylRawDB-method	getData-methods
getDBPath	getDBPath-methods
getDBPath,methylBaseDB-method	getDBPath-methods
getDBPath,methylDiffDB-method	getDBPath-methods
getDBPath,methylRawDB-method	getDBPath-methods
getDBPath,methylRawListDB-method	getDBPath-methods
getFeatsWithTargetsStats	methylKit-defunct
getFlanks	methylKit-defunct
getMembers	methylKit-defunct
getMethylationStats	getMethylationStats-methods
getMethylationStats,methylRaw-method	getMethylationStats-methods
getMethylationStats,methylRawDB-method	getMethylationStats-methods
getMethylDiff	getMethylDiff-methods
getMethylDiff,methylDiff-method	getMethylDiff-methods
getMethylDiff,methylDiffDB-method	getMethylDiff-methods
getSampleID	getSampleID-methods
getSampleID,methylBase-method	getSampleID-methods
getSampleID,methylBaseDB-method	getSampleID-methods
getSampleID,methylDiff-method	getSampleID-methods
getSampleID,methylDiffDB-method	getSampleID-methods
getSampleID,methylRaw-method	getSampleID-methods
getSampleID,methylRawDB-method	getSampleID-methods
getSampleID,methylRawList-method	getSampleID-methods
getSampleID,methylRawListDB-method	getSampleID-methods
getSampleID<-	getSampleID-methods
getSampleID<-,methylBase-method	getSampleID-methods
getSampleID<-,methylBaseDB-method	getSampleID-methods
getSampleID<-,methylDiff-method	getSampleID-methods
getSampleID<-,methylDiffDB-method	getSampleID-methods
getSampleID<-,methylRaw-method	getSampleID-methods
getSampleID<-,methylRawDB-method	getSampleID-methods
getSampleID<-,methylRawList-method	getSampleID-methods
getSampleID<-,methylRawListDB-method	getSampleID-methods
getTargetAnnotationStats	methylKit-defunct
getTreatment	getTreatment-methods
getTreatment,getTreatment,methylDiffDB-method	getTreatment-methods
getTreatment,methylBase-method	getTreatment-methods
getTreatment,methylBaseDB-method	getTreatment-methods
getTreatment,methylDiff-method	getTreatment-methods
getTreatment,methylDiffDB-method	getTreatment-methods
getTreatment,methylRawList-method	getTreatment-methods
getTreatment,methylRawListDB-method	getTreatment-methods
getTreatment<-	getTreatment-methods
getTreatment<-,methylBase-method	getTreatment-methods
getTreatment<-,methylBaseDB-method	getTreatment-methods
getTreatment<-,methylDiff-method	getTreatment-methods
getTreatment<-,methylDiffDB-method	getTreatment-methods
getTreatment<-,methylRawList-method	getTreatment-methods
getTreatment<-,methylRawListDB-method	getTreatment-methods
joinSegmentNeighbours	joinSegmentNeighbours
makeMethylDB	makeMethylDB-methods
makeMethylDB,methylBase-method	makeMethylDB-methods
makeMethylDB,methylBase-methods	makeMethylDB-methods
makeMethylDB,methylDiff-method	makeMethylDB-methods
makeMethylDB,methylDiff-methods	makeMethylDB-methods
makeMethylDB,methylRaw-method	makeMethylDB-methods
makeMethylDB,methylRaw-methods	makeMethylDB-methods
makeMethylDB,methylRawList-method	makeMethylDB-methods
makeMethylDB,methylRawList-methods	makeMethylDB-methods
methRead	methRead-methods
methRead,character,ANY,ANY-method	methRead-methods
methRead,character,character,character-method	methRead-methods
methRead,character-method	methRead-methods
methRead,list,ANY,ANY-method	methRead-methods
methRead,list,list,character-method	methRead-methods
methSeg	methSeg
methSeg2bed	methSeg2bed
methylBase	methylBase-class
methylBase-class	methylBase-class
methylBase.obj	methylBase.obj
methylBaseDB	methylBaseDB-class
methylBaseDB-class	methylBaseDB-class
methylDiff	methylDiff-class
methylDiff-class	methylDiff-class
methylDiff.obj	methylDiff.obj
methylDiffDB	methylDiffDB-class
methylDiffDB-class	methylDiffDB-class
methylKit-defunct	methylKit-defunct
methylRaw	methylRaw-class
methylRaw-class	methylRaw-class
methylRawDB	methylRawDB-class
methylRawDB-class	methylRawDB-class
methylRawList	methylRawList-class
methylRawList-class	methylRawList-class
methylRawList.obj	methylRawList.obj
methylRawListDB	methylRawListDB-class
methylRawListDB-class	methylRawListDB-class
normalizeCoverage	normalizeCoverage-methods
normalizeCoverage,methylRawList-method	normalizeCoverage-methods
normalizeCoverage,methylRawListDB-method	normalizeCoverage-methods
PCASamples	PCASamples-methods
PCASamples,methylBase-method	PCASamples-methods
PCASamples,methylBaseDB-method	PCASamples-methods
percMethylation	percMethylation-methods
percMethylation,methylBase-method	percMethylation-methods
percMethylation,methylBaseDB-method	percMethylation-methods
plotTargetAnnotation	methylKit-defunct
pool	pool-methods
pool,methylBase-method	pool-methods
pool,methylBaseDB-method	pool-methods
processBismarkAln	processBismarkAln-methods
processBismarkAln,character,character,character-method	processBismarkAln-methods
processBismarkAln,list,list,character-method	processBismarkAln-methods
read	methylKit-defunct
read.bed	methylKit-defunct
read.bismark	methylKit-defunct
read.feature.flank	methylKit-defunct
read.transcript.features	methylKit-defunct
readMethylDB	readMethylDB-methods
reconstruct	reconstruct-methods
reconstruct,ANY,methylBase-method	reconstruct-methods
reconstruct,ANY,methylBaseDB-method	reconstruct-methods
reconstruct,methylBase-method	reconstruct-methods
reconstruct,methylBaseDB-method	reconstruct-methods
regionCounts	regionCounts
regionCounts,methylBase,GRanges-method	regionCounts
regionCounts,methylBase,GRangesList-method	regionCounts
regionCounts,methylBaseDB,GRanges-method	regionCounts
regionCounts,methylBaseDB,GRangesList-method	regionCounts
regionCounts,methylRaw,GRanges-method	regionCounts
regionCounts,methylRaw,GRangesList-method	regionCounts
regionCounts,methylRawDB,GRanges-method	regionCounts
regionCounts,methylRawDB,GRangesList-method	regionCounts
regionCounts,methylRawList,GRanges-method	regionCounts
regionCounts,methylRawList,GRangesList-method	regionCounts
regionCounts,methylRawListDB,GRanges-method	regionCounts
regionCounts,methylRawListDB,GRangesList-method	regionCounts
removeComp	removeComp-methods
removeComp,methylBase-method	removeComp-methods
removeComp,methylBaseDB-method	removeComp-methods
reorganize	reorganize-methods
reorganize,methylBase-method	reorganize-methods
reorganize,methylBaseDB-method	reorganize-methods
reorganize,methylRawList-method	reorganize-methods
reorganize,methylRawListDB-method	reorganize-methods
select	select-methods
select,methylBase-method	select-methods
select,methylBaseDB-method	select-methods
select,methylDiff-method	select-methods
select,methylDiffDB-method	select-methods
select,methylRaw-method	select-methods
select,methylRawDB-method	select-methods
selectByOverlap	selectByOverlap-methods
selectByOverlap,methylBase,GRanges-method	selectByOverlap-methods
selectByOverlap,methylBase-method	selectByOverlap-methods
selectByOverlap,methylBaseDB,GRanges-method	selectByOverlap-methods
selectByOverlap,methylBaseDB-method	selectByOverlap-methods
selectByOverlap,methylDiff,GRanges-method	selectByOverlap-methods
selectByOverlap,methylDiff-method	selectByOverlap-methods
selectByOverlap,methylDiffDB,GRanges-method	selectByOverlap-methods
selectByOverlap,methylDiffDB-method	selectByOverlap-methods
selectByOverlap,methylRaw,GRanges-method	selectByOverlap-methods
selectByOverlap,methylRaw-method	selectByOverlap-methods
selectByOverlap,methylRawDB,GRanges-method	selectByOverlap-methods
selectByOverlap,methylRawDB-method	selectByOverlap-methods
selectByOverlap,methylRawList,GRanges-method	selectByOverlap-methods
selectByOverlap,methylRawList-method	selectByOverlap-methods
selectByOverlap,methylRawListDB,GRanges-method	selectByOverlap-methods
selectByOverlap,methylRawListDB-method	selectByOverlap-methods
show,methylBase	show-methods
show,methylBase-method	show-methods
show,methylBaseDB	show-methods
show,methylBaseDB-method	show-methods
show,methylDiff	show-methods
show,methylDiff-method	show-methods
show,methylDiffDB	show-methods
show,methylDiffDB-method	show-methods
show,methylRaw	show-methods
show,methylRaw-method	show-methods
show,methylRawDB	show-methods
show,methylRawDB-method	show-methods
show,methylRawList	show-methods
show,methylRawList-method	show-methods
show,methylRawListDB	show-methods
show,methylRawListDB-method	show-methods
tileMethylCounts	tileMethylCounts-methods
tileMethylCounts,methylBase-method	tileMethylCounts-methods
tileMethylCounts,methylBaseDB-method	tileMethylCounts-methods
tileMethylCounts,methylRaw-method	tileMethylCounts-methods
tileMethylCounts,methylRawDB-method	tileMethylCounts-methods
tileMethylCounts,methylRawList-method	tileMethylCounts-methods
tileMethylCounts,methylRawListDB-method	tileMethylCounts-methods
unite	unite-methods
unite,methylRawList-method	unite-methods
unite,methylRawListDB-method	unite-methods
updateMethObject	updateMethObject
[,methylBase,ANY,ANY,ANY-method	extract-methods
[,methylBaseDB,ANY,ANY,ANY-method	extract-methods
[,methylDiff,ANY,ANY,ANY-method	extract-methods
[,methylDiffDB,ANY,ANY,ANY-method	extract-methods
[,methylRaw,ANY,ANY,ANY-method	extract-methods
[,methylRawDB,ANY,ANY,ANY-method	extract-methods
