DMCHMM-package	DMCHMM-package
BSData	BSData-class
BSData-class	BSData-class
BSDMCs	BSDMCs-class
BSDMCs-class	BSDMCs-class
cBSData	cBSData-method
cBSData,matrix,matrix,GRanges-method	cBSData-method
cBSData-method	cBSData-method
cBSDMCs	cBSDMCs-method
cBSDMCs,matrix,matrix,matrix,matrix,matrix,GRanges-method	cBSDMCs-method
cBSDMCs-method	cBSDMCs-method
combine	combine-method
combine,BSData,BSData-method	combine-method
combine,BSDMCs,BSDMCs-method	combine-method
combine-method	combine-method
data	data
DMCHMM	DMCHMM-package
findDMCs	findDMCs-method
findDMCs,BSDMCs-method	findDMCs-method
findDMCs-method	findDMCs-method
manhattanDMCs	manhattanDMCs-method
manhattanDMCs,BSDMCs-method	manhattanDMCs-method
manhattanDMCs-method	manhattanDMCs-method
methHMEM	methHMEM-method
methHMEM,BSData-method	methHMEM-method
methHMEM-method	methHMEM-method
methHMMCMC	methHMMCMC-method
methHMMCMC,BSDMCs-method	methHMMCMC-method
methHMMCMC-method	methHMMCMC-method
methLevels	methLevels-method
methLevels,BSDMCs-method	methLevels-method
methLevels-method	methLevels-method
methLevels<-	methLevels-method
methLevels<-,BSDMCs,matrix-method	methLevels-method
methReads	methReads-method
methReads,BSData-method	methReads-method
methReads,BSDMCs-method	methReads-method
methReads-method	methReads-method
methReads<-	methReads-method
methReads<-,BSData,matrix-method	methReads-method
methReads<-,BSDMCs,matrix-method	methReads-method
methStates	methStates-method
methStates,BSDMCs-method	methStates-method
methStates-method	methStates-method
methStates<-	methStates-method
methStates<-,BSDMCs,matrix-method	methStates-method
methVars	methVars-method
methVars,BSDMCs-method	methVars-method
methVars-method	methVars-method
methVars<-	methVars-method
methVars<-,BSDMCs,matrix-method	methVars-method
params	params
qqDMCs	qqDMCs-method
qqDMCs,BSDMCs-method	qqDMCs-method
qqDMCs-method	qqDMCs-method
readBismark	readBismark-method
readBismark,character,character,numeric-method	readBismark-method
readBismark,character,data.frame,numeric-method	readBismark-method
readBismark,character,DataFrame,numeric-method	readBismark-method
readBismark-method	readBismark-method
totalReads	totalReads-method
totalReads,BSData-method	totalReads-method
totalReads,BSDMCs-method	totalReads-method
totalReads-method	totalReads-method
totalReads<-	totalReads-method
totalReads<-,BSData,matrix-method	totalReads-method
totalReads<-,BSDMCs,matrix-method	totalReads-method
writeBED	writeBED-method
writeBED,BSData,character,character-method	writeBED-method
writeBED,BSData,character,missing-method	writeBED-method
writeBED,BSData,missing,character-method	writeBED-method
writeBED,BSData,missing,missing-method	writeBED-method
writeBED,BSDMCs,character,character-method	writeBED-method
writeBED,BSDMCs,character,missing-method	writeBED-method
writeBED,BSDMCs,missing,character-method	writeBED-method
writeBED,BSDMCs,missing,missing-method	writeBED-method
writeBED-method	writeBED-method
