segmentSeq-package	segmentSeq-package
alignmentData	alignmentData-class
alignmentData-class	alignmentData-class
cbind	alignmentData-class
cbind,alignmentData-method	alignmentData-class
classifySeg	classifySeg
dim,alignmentData-method	alignmentData-class
dim,postSeg-method	postSeg-class
dim,segData-method	segData-class
filterSegments	filterSegments
findChunks	findChunks
getCounts	getCounts
getOverlaps	getOverlaps
heuristicSeg	heuristicSeg
initialize,alignmentData-method	alignmentData-class
initialize,segData-method	segData-class
lociLikelihoods	lociLikelihoods
mergeSD	mergeSD
plotGenome	plotGenome
postSeg	postSeg-class
postSeg-class	postSeg-class
processAD	processAD
processTags	processTags
segData-class	segData-class
segmentSeq	segmentSeq-package
show,alignmentData-method	alignmentData-class
show,postSeg-method	postSeg-class
show,segData-method	segData-class
SL10	SL
SL26	SL
SL32	SL
SL9	SL
[,alignmentData,ANY,ANY-method	alignmentData-class
[,alignmentData-method	alignmentData-class
[,postSeg-method	postSeg-class
[,segData,ANY,ANY-method	segData-class
[,segData-method	segData-class
