API for DMCHMM
Differentially Methylated CpG using Hidden Markov Model

Global functions
.EMHMM.M	Source code
.HMMmcmc.M	Source code
.cBSDMCs	Source code
.cBSData	Source code
.combine.BSDMCs	Source code
.combine.BSData	Source code
.findDMCs	Source code
.manhattanDMCs	Source code
.marglike	Source code
.marglike.M	Source code
.methHMEM	Source code
.methHMMCMC	Source code
.methLevels	Source code
.methReads	Source code
.methStates	Source code
.methVars	Source code
.onAttach	Source code
.qqDMCs	Source code
.readBismark	Source code
.replace.methLevels	Source code
.replace.methReads	Source code
.replace.methStates	Source code
.replace.methVars	Source code
.replace.totalReads	Source code
.runEM.M	Source code
.runMCMC.M	Source code
.totalReads	Source code
.writeBED_BSDMCs	Source code
.writeBED_BSData	Source code
BSDMCs	Man page
BSDMCs-class	Man page
BSData	Man page
BSData-class	Man page
DMCHMM	Man page
DMCHMM-package	Man page
cBSDMCs	Man page
cBSDMCs,matrix,matrix,matrix,matrix,matrix,GRanges-method	Man page
cBSDMCs-method	Man page
cBSData	Man page
cBSData,matrix,matrix,GRanges-method	Man page
cBSData-method	Man page
combine	Man page
combine,BSDMCs,BSDMCs-method	Man page
combine,BSData,BSData-method	Man page
combine-method	Man page
data	Man page
findDMCs	Man page
findDMCs,BSDMCs-method	Man page
findDMCs-method	Man page
manhattanDMCs	Man page
manhattanDMCs,BSDMCs-method	Man page
manhattanDMCs-method	Man page
methHMEM	Man page
methHMEM,BSData-method	Man page
methHMEM-method	Man page
methHMMCMC	Man page
methHMMCMC,BSDMCs-method	Man page
methHMMCMC-method	Man page
methLevels	Man page
methLevels,BSDMCs-method	Man page
methLevels-method	Man page
methLevels<-	Man page
methLevels<-,BSDMCs,matrix-method	Man page
methReads	Man page
methReads,BSDMCs-method	Man page
methReads,BSData-method	Man page
methReads-method	Man page
methReads<-	Man page
methReads<-,BSDMCs,matrix-method	Man page
methReads<-,BSData,matrix-method	Man page
methStates	Man page
methStates,BSDMCs-method	Man page
methStates-method	Man page
methStates<-	Man page
methStates<-,BSDMCs,matrix-method	Man page
methVars	Man page
methVars,BSDMCs-method	Man page
methVars-method	Man page
methVars<-	Man page
methVars<-,BSDMCs,matrix-method	Man page
params	Man page
qqDMCs	Man page
qqDMCs,BSDMCs-method	Man page
qqDMCs-method	Man page
readBismark	Man page
readBismark,character,DataFrame,numeric-method	Man page
readBismark,character,character,numeric-method	Man page
readBismark,character,data.frame,numeric-method	Man page
readBismark-method	Man page
totalReads	Man page
totalReads,BSDMCs-method	Man page
totalReads,BSData-method	Man page
totalReads-method	Man page
totalReads<-	Man page
totalReads<-,BSDMCs,matrix-method	Man page
totalReads<-,BSData,matrix-method	Man page
writeBED	Man page
writeBED,BSDMCs,character,character-method	Man page
writeBED,BSDMCs,character,missing-method	Man page
writeBED,BSDMCs,missing,character-method	Man page
writeBED,BSDMCs,missing,missing-method	Man page
writeBED,BSData,character,character-method	Man page
writeBED,BSData,character,missing-method	Man page
writeBED,BSData,missing,character-method	Man page
writeBED,BSData,missing,missing-method	Man page
writeBED-method	Man page