methylPipe-package	methylPipe-package
$,BSdataSet	BSdataSet-class
$,BSdataSet-method	BSdataSet-class
$,GElist	GElist-class
$,GElist-method	GElist-class
binC	GEcollection-class
binC,GEcollection-method	GEcollection-class
binmC	GEcollection-class
binmC,GEcollection-method	GEcollection-class
binrC	GEcollection-class
binrC,GEcollection-method	GEcollection-class
binscore	GEcollection-class
binscore,GEcollection-method	GEcollection-class
binscore<-	GEcollection-class
binscore<-,GEcollection-method	GEcollection-class
BSdata	BSdata-class
BSdata-class	BSdata-class
BSdataSet	BSdataSet-class
BSdataSet-class	BSdataSet-class
BSprepare	BSprepare
chiCombP	chiCombP
chr	GEcollection-class
chr,GEcollection-method	GEcollection-class
consolidateDMRs	consolidateDMRs
extractBinGRanges	extractBinGRanges
findDMR	findDMR
findDMR,BSdataSet-method	findDMR
findDMR,methylPipe,BSdataSet	findDMR
findDMR,methylPipe,BSdataSet-method	findDMR
findDMR-methods	findDMR
findPMDs	findPMDs
findPMDs,BSdata-method	findPMDs
findPMDs,methylPipe,BSdata	findPMDs
findPMDs,methylPipe,BSdata-method	findPMDs
findPMDs-methods	findPMDs
GEcollection	GEcollection-class
GEcollection-class	GEcollection-class
GElist	GElist-class
GElist-class	GElist-class
getCpos	getCpos
getCposChr	getCpos
getCposDensity	getCposDensity
length	GEcollection-class
length,BSdataSet-method	BSdataSet-class
length,GEcollection-method	GEcollection-class
length,GElist-method	GElist-class
mapBSdata2GRanges	mapBSdata2GRanges
mapBSdata2GRangesBin	mapBSdata2GRanges
mCsmoothing	mCsmoothing
mCsmoothing,BSdata-method	mCsmoothing
mCsmoothing,methylPipe,BSdata	mCsmoothing
mCsmoothing,methylPipe,BSdata-method	mCsmoothing
mCsmoothing-methods	mCsmoothing
meth.call	meth.call
methstats	methstats
methstats,BSdataSet-method	methstats
methstats,methylPipe,BSdataSet	methstats
methstats,methylPipe,BSdataSet-method	methstats
methstats-methods	methstats
methylPipe	methylPipe-package
nbins	GEcollection-class
nbins,GEcollection-method	GEcollection-class
plotMeth	plotMeth
process.hmc	process.hmc
profileDNAmetBin	profileDNAmetBin
profileDNAmetBinParallel	profileDNAmetBin
show,BSdata-method	BSdata-class
show,BSdataSet-method	BSdataSet-class
show,GEcollection-method	GEcollection-class
show,GElist-method	GElist-class
splitChrs	splitChrs
tabixdata2GR	tabixdata2GR
[,BSdataSet,ANY,ANY-method	BSdataSet-class
[,GElist,ANY,ANY-method	GElist-class
[[,BSdataSet,ANY,ANY-method	BSdataSet-class
[[,GElist,ANY,ANY-method	GElist-class
[[<-,BSdataSet,ANY,ANY-method	BSdataSet-class
[[<-,GElist,ANY,ANY-method	GElist-class
