assayNames,BSseq-method	BSseq-class
assays,BSseq-method	BSseq-class
binomialGoodnessOfFit	goodnessOfFit
BS.chr22	BS.chr22
BSmooth	BSmooth
BSmooth.fstat	BSmooth.fstat
BSmooth.tstat	BSmooth.tstat
BSseq	BSseq
BSseq-class	BSseq-class
bsseq-deprecated	bsseq-deprecated
BSseqStat	BSseqStat-class
BSseqStat-class	BSseqStat-class
BSseqTstat	BSseqTstat-class
BSseqTstat-class	BSseqTstat-class
chisqGoodnessOfFit	goodnessOfFit
chrSelectBSseq	BSseq-class
class:hasGRanges	hasGRanges-class
collapseBSseq	BSseq-class
combine,BSseq,BSseq-method	BSseq-class
combineList	BSseq-class
computeStat	computeStat
data.frame2GRanges	data.frame2GRanges
dimnames,arrayRealizationSink-method	FWGRanges-class
dmrFinder	dmrFinder
end,FWGRanges-method	FWGRanges-class
end,FWIRanges-method	FWGRanges-class
end,hasGRanges-method	hasGRanges-class
end<-,FWIRanges-method	FWGRanges-class
end<-,hasGRanges-method	hasGRanges-class
estimateErrorRate	estimateErrorRate
findLoci	findLoci
findOverlaps,FWGRanges,FWGRanges-method	FWGRanges-class
findOverlaps,GenomicRanges,hasGRanges-method	hasGRanges-class
findOverlaps,hasGRanges,GenomicRanges-method	hasGRanges-class
findOverlaps,hasGRanges,hasGRanges-method	hasGRanges-class
fisherTests	fisherTests
FWGRanges-class	FWGRanges-class
FWIRanges-class	FWGRanges-class
getBSseq	BSseq-class
getCoverage	getCoverage
getCpGMatrix	getCpGMatrix
getCpGs	getCpGs
getMaxLikelihoodMatrix	getMaxLikelihoodMatrix
getMeth	getMeth
getStats	getStats
granges,hasGRanges-method	hasGRanges-class
hasBeenSmoothed	BSseq-class
hasGRanges	hasGRanges-class
hasGRanges-class	hasGRanges-class
length,BSseq-method	BSseq-class
length,hasGRanges-method	hasGRanges-class
matrixOrNULL-class	internals
names,FWIRanges-method	FWGRanges-class
names<-,FWIRanges-method	FWGRanges-class
orderBSseq	BSseq-class
overlapsAny,GenomicRanges,hasGRanges-method	hasGRanges-class
overlapsAny,hasGRanges,GenomicRanges-method	hasGRanges-class
overlapsAny,hasGRanges,hasGRanges-method	hasGRanges-class
pData,BSseq-method	BSseq-class
pData<-,BSseq,data.frame-method	BSseq-class
pData<-,BSseq,DataFrame-method	BSseq-class
plot.chisqGoodnessOfFit	goodnessOfFit
plotManyRegions	plotRegion
plotRegion	plotRegion
poissonGoodnessOfFit	goodnessOfFit
print.chisqGoodnessOfFit	goodnessOfFit
read.bedMethyl	read.bedMethyl
read.bismark	read.bismark
sampleNames,BSseq-method	BSseq-class
sampleNames<-,BSseq,ANY-method	BSseq-class
seqlengths,hasGRanges-method	hasGRanges-class
seqlengths<-,hasGRanges-method	hasGRanges-class
seqlevels,hasGRanges-method	hasGRanges-class
seqlevels<-,hasGRanges-method	hasGRanges-class
seqnames,FWGRanges-method	FWGRanges-class
seqnames,hasGRanges-method	hasGRanges-class
seqnames<-,hasGRanges-method	hasGRanges-class
show,BSseq-method	BSseq-class
show,BSseqStat-method	BSseqStat-class
show,BSseqTstat-method	BSseqTstat-class
smoothSds	smoothSds
start,FWGRanges-method	FWGRanges-class
start,FWIRanges-method	FWGRanges-class
start,hasGRanges-method	hasGRanges-class
start<-,FWIRanges-method	FWGRanges-class
start<-,hasGRanges-method	hasGRanges-class
strand,FWGRanges-method	FWGRanges-class
strand,hasGRanges-method	hasGRanges-class
strand<-,hasGRanges,ANY-method	hasGRanges-class
strand<-,hasGRanges-method	hasGRanges-class
strandCollapse	BSseq-class
subsetByOverlaps,GenomicRanges,hasGRanges-method	hasGRanges-class
subsetByOverlaps,hasGRanges,GenomicRanges-method	hasGRanges-class
subsetByOverlaps,hasGRanges,hasGRanges-method	hasGRanges-class
updateObject,BSseq-method	BSseq-class
updateObject,BSseqStat-method	BSseqStat-class
updateObject,BSseqTstat-method	BSseqTstat-class
width,FWGRanges-method	FWGRanges-class
width,FWIRanges-method	FWGRanges-class
width,hasGRanges-method	hasGRanges-class
width<-,FWIRanges-method	FWGRanges-class
width<-,hasGRanges-method	hasGRanges-class
[,BSseq-method	BSseq-class
[,BSseqStat,ANY,ANY,ANY-method	BSseqStat-class
[,BSseqStat-method	BSseqStat-class
[,BSseqTstat,ANY,ANY,ANY-method	BSseqTstat-class
[,BSseqTstat-method	BSseqTstat-class
[,hasGRanges,ANY,ANY,ANY-method	hasGRanges-class
[,hasGRanges-method	hasGRanges-class
