annotateGRanges	annotateGRanges
annotateGRanges,GRanges,GRanges,character,character-method	annotateGRanges
annotateGRanges,GRanges,GRanges,character,integer-method	annotateGRanges
annotateGRanges,GRanges,GRanges,character,missing-method	annotateGRanges
betaRegression	betaRegression
betaRegression,formula,character,BSrel,missing-method	betaRegression
betaRegression,formula,character,BSrel,numeric-method	betaRegression
betaResults	betaResults
betaResultsNull	betaResultsNull
binomLikelihoodSmooth	binomLikelihoodSmooth
binomLikelihoodSmooth,ANY-method	binomLikelihoodSmooth
BSraw	BSraw-class
BSraw,matrix,matrix,GRanges-method	BSraw-class
BSraw-class	BSraw-class
BSrel	BSrel-class
BSrel,matrix,GRanges-method	BSrel-class
BSrel-class	BSrel-class
clusterSites	clusterSites
clusterSites,BSraw,ANY,numeric,missing,missing,missing-method	clusterSites
clusterSites,BSraw,ANY,numeric,missing,numeric,missing-method	clusterSites
clusterSites,BSraw,ANY,numeric,numeric,missing,missing-method	clusterSites
clusterSites,BSraw,ANY,numeric,numeric,numeric,missing-method	clusterSites
clusterSites,BSraw,ANY,numeric,numeric,numeric,numeric-method	clusterSites
clusterSites,BSraw,missing,missing,missing,missing,missing-method	clusterSites
clusterSites,BSraw,missing,numeric,numeric,numeric,missing-method	clusterSites
clusterSites,BSraw,missing,numeric,numeric,numeric,numeric-method	clusterSites
clusterSitesToGR	clusterSitesToGR
clusterSitesToGR,BSraw-method	clusterSitesToGR
clusterSitesToGR,BSrel-method	clusterSitesToGR
combine,BSraw,BSraw-method	BSraw-class
combine,BSrel,BSrel-method	BSrel-class
compareTwoSamples	compareTwoSamples
compareTwoSamples,BSraw,character,character,numeric,numeric-method	compareTwoSamples
compareTwoSamples,BSraw,numeric,numeric,numeric,numeric-method	compareTwoSamples
compareTwoSamples,BSrel,character,character,numeric,numeric-method	compareTwoSamples
compareTwoSamples,BSrel,numeric,numeric,numeric,numeric-method	compareTwoSamples
covBoxplots	covBoxplots
covBoxplots,BSraw-method	covBoxplots
covStatistics	covStatistics
covStatistics,BSraw-method	covStatistics
covStatistics,BSrel-method	covStatistics
DMRs	DMRs
estLocCor	estLocCor
estLocCor,list-method	estLocCor
filterByCov	filterByCov
filterByCov,BSraw,missing,logical-method	filterByCov
filterByCov,BSraw,missing,missing-method	filterByCov
filterByCov,BSraw,numeric,logical-method	filterByCov
filterByCov,BSraw,numeric,missing-method	filterByCov
filterBySharedRegions	filterBySharedRegions
filterBySharedRegions,BSraw,ANY,missing,numeric,missing-method	filterBySharedRegions
filterBySharedRegions,BSraw,ANY,missing,numeric,numeric-method	filterBySharedRegions
filterBySharedRegions,BSraw,ANY,numeric,missing,missing-method	filterBySharedRegions
filterBySharedRegions,BSraw,ANY,numeric,missing,numeric-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,missing,missing,missing-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,missing,missing,numeric-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,missing,numeric,missing-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,missing,numeric,numeric-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,numeric,missing,missing-method	filterBySharedRegions
filterBySharedRegions,BSraw,missing,numeric,missing,numeric-method	filterBySharedRegions
filterBySharedRegions,BSrel,ANY,missing,numeric,ANY-method	filterBySharedRegions
filterBySharedRegions,BSrel,ANY,numeric,missing,ANY-method	filterBySharedRegions
filterBySharedRegions,BSrel,missing,missing,missing,ANY-method	filterBySharedRegions
filterBySharedRegions,BSrel,missing,missing,numeric,ANY-method	filterBySharedRegions
filterBySharedRegions,BSrel,missing,numeric,missing,ANY-method	filterBySharedRegions
findDMRs	findDMRs
findDMRs,data.frame,missing,numeric,logical-method	findDMRs
findDMRs,data.frame,missing,numeric,missing-method	findDMRs
findDMRs,data.frame,numeric,numeric,logical-method	findDMRs
findDMRs,data.frame,numeric,numeric,missing-method	findDMRs
globalTest	globalTest
globalTest,ANY,BSrel-method	globalTest
limitCov	limitCov
limitCov,BSraw,numeric-method	limitCov
logisticRegression	logisticRegression
logisticRegression,formula,character,BSrel,missing-method	logisticRegression
logisticRegression,formula,character,BSrel,numeric-method	logisticRegression
makeVariogram	makeVariogram
makeVariogram,data.frame,logical,missing,missing-method	makeVariogram
makeVariogram,data.frame,logical,missing,numeric-method	makeVariogram
makeVariogram,data.frame,logical,numeric,missing-method	makeVariogram
makeVariogram,data.frame,logical,numeric,numeric-method	makeVariogram
makeVariogram,data.frame,missing,missing,missing-method	makeVariogram
makeVariogram,data.frame,missing,numeric,numeric-method	makeVariogram
methLevel	BSrel-class
methLevel,BSrel-method	BSrel-class
methLevel<-	BSrel-class
methLevel<-,BSrel,matrix-method	BSrel-class
methReads	BSraw-class
methReads,BSraw-method	BSraw-class
methReads<-	BSraw-class
methReads<-,BSraw,matrix-method	BSraw-class
plotBindingSites	plotBindingSites
plotBindingSites,BSraw,GRanges-method	plotBindingSites
plotBindingSites,BSrel,GRanges-method	plotBindingSites
plotMeth	plotMeth
plotMeth,BSraw,BSrel,GRanges-method	plotMeth
plotMethMap	plotMethMap
plotMethMap,BSraw,GRanges,factor,logical-method	plotMethMap
plotMethMap,BSraw,GRanges,factor,missing-method	plotMethMap
plotMethMap,BSraw,GRanges,missing,logical-method	plotMethMap
plotMethMap,BSraw,GRanges,missing,missing-method	plotMethMap
plotMethMap,BSrel,GRanges,factor,logical-method	plotMethMap
plotMethMap,BSrel,GRanges,factor,missing-method	plotMethMap
plotMethMap,BSrel,GRanges,missing,logical-method	plotMethMap
plotMethMap,BSrel,GRanges,missing,missing-method	plotMethMap
plotSmoothMeth	plotSmoothMeth
plotSmoothMeth,BSrel,GRanges,ANY,logical-method	plotSmoothMeth
plotSmoothMeth,BSrel,GRanges,ANY,missing-method	plotSmoothMeth
predictedMeth	predictedMeth
predictMeth	predictMeth
predictMeth,BSraw,missing,missing,missing-method	predictMeth
predictMeth,BSraw,missing,missing,numeric-method	predictMeth
predictMeth,BSraw,numeric,missing,missing-method	predictMeth
predictMeth,BSraw,numeric,missing,numeric-method	predictMeth
predictMeth,BSraw,numeric,numeric,numeric-method	predictMeth
promoters	promoters
rawToRel	rawToRel
rawToRel,BSraw-method	rawToRel
readBismark	readBismark
readBismark,character,character-method	readBismark
readBismark,character,data.frame-method	readBismark
readBismark,character,DataFrame-method	readBismark
rrbs	rrbs
smoothVariogram	smoothVariogram
smoothVariogram,list,numeric,missing-method	smoothVariogram
smoothVariogram,list,numeric,numeric-method	smoothVariogram
smoothVariogram,matrix,numeric,missing-method	smoothVariogram
smoothVariogram,matrix,numeric,numeric-method	smoothVariogram
summarizeRegions	summarizeRegions
summarizeRegions,BSraw,GRanges,logical-method	summarizeRegions
summarizeRegions,BSraw,GRanges,missing-method	summarizeRegions
summarizeRegions,BSrel,GRanges,logical-method	summarizeRegions
summarizeRegions,BSrel,GRanges,missing-method	summarizeRegions
testClusters	testClusters
testClusters,list,missing-method	testClusters
testClusters,list,numeric-method	testClusters
totalReads	BSraw-class
totalReads,BSraw-method	BSraw-class
totalReads<-	BSraw-class
totalReads<-,BSraw,matrix-method	BSraw-class
trimClusters	trimClusters
trimClusters,list,missing-method	trimClusters
trimClusters,list,numeric-method	trimClusters
vario	vario
writeBED	writeBED
writeBED,BSraw,character,character-method	writeBED
writeBED,BSraw,character,missing-method	writeBED
writeBED,BSraw,missing,character-method	writeBED
writeBED,BSraw,missing,missing-method	writeBED
writeBED,BSrel,character,character-method	writeBED
writeBED,BSrel,character,missing-method	writeBED
writeBED,BSrel,missing,character-method	writeBED
writeBED,BSrel,missing,missing-method	writeBED
