checkRestrictionEnzymeSequence	checkRestrictionEnzymeSequence
checkRestrictionEnzymeSequence,character,character-method	checkRestrictionEnzymeSequence
chooseNearCisFragments	chooseNearCisFragments
chooseNearCisFragments,Data4Cseq,numeric-method	chooseNearCisFragments
createVirtualFragmentLibrary	createVirtualFragmentLibrary
createVirtualFragmentLibrary,BSgenome,character,character,numeric-method	createVirtualFragmentLibrary
createVirtualFragmentLibrary,DNAString,character,character,numeric-method	createVirtualFragmentLibrary
Data4Cseq	Data4Cseq
Data4Cseq,character,numeric,numeric,data.frame,GAlignments-method	Data4Cseq
Data4Cseq,character,numeric,numeric,missing,missing-method	Data4Cseq
Data4Cseq-class	Data4Cseq-class
drawDigestionFragmentHistogram	drawDigestionFragmentHistogram
drawDigestionFragmentHistogram,data.frame-method	drawDigestionFragmentHistogram
drawHeatmap	drawHeatmap
drawHeatmap,data.frame-method	drawHeatmap
drawHeatmap,Data4Cseq-method	drawHeatmap
exportVisualizationFragmentData	exportVisualizationFragmentData
exportVisualizationFragmentData,Data4Cseq,character-method	exportVisualizationFragmentData
getReadDistribution	getReadDistribution
getReadDistribution,Data4Cseq-method	getReadDistribution
giveEnzymeSequence	giveEnzymeSequence
giveEnzymeSequence,character,character-method	giveEnzymeSequence
importVisualizationFragmentData	importVisualizationFragmentData
importVisualizationFragmentData,character-method	importVisualizationFragmentData
liverData	liverData
liverDataRaw	liverDataRaw
nearCisFragments	Data4Cseq-class
nearCisFragments,Data4Cseq-method	Data4Cseq-class
nearCisFragments<-	Data4Cseq-class
nearCisFragments<-,Data4Cseq,data.frame-method	Data4Cseq-class
normalizeFragmentData	normalizeFragmentData
normalizeFragmentData,Data4Cseq-method	normalizeFragmentData
plotTransInteractions	plotTransInteractions
plotTransInteractions,character,character,numeric,character-method	plotTransInteractions
plotTransInteractions,data.frame,character,numeric,data.frame-method	plotTransInteractions
pointsOfInterest	Data4Cseq-class
pointsOfInterest,Data4Cseq-method	Data4Cseq-class
pointsOfInterest<-	Data4Cseq-class
pointsOfInterest<-,Data4Cseq,data.frame-method	Data4Cseq-class
prepare4CseqData	prepare4CseqData
prepare4CseqData,character,character,character,character-method	prepare4CseqData
printBEDFragmentLibrary	printBEDFragmentLibrary
printBEDFragmentLibrary,character,character-method	printBEDFragmentLibrary
printWigFile	printWigFile
printWigFile,Data4Cseq-method	printWigFile
rawFragments	Data4Cseq-class
rawFragments,Data4Cseq-method	Data4Cseq-class
rawFragments<-	Data4Cseq-class
rawFragments<-,Data4Cseq,data.frame-method	Data4Cseq-class
rawReads	Data4Cseq-class
rawReads,Data4Cseq-method	Data4Cseq-class
rawReads<-	Data4Cseq-class
rawReads<-,Data4Cseq,GAlignments-method	Data4Cseq-class
readLength	Data4Cseq-class
readLength,Data4Cseq-method	Data4Cseq-class
readLength<-	Data4Cseq-class
readLength<-,Data4Cseq,numeric-method	Data4Cseq-class
readPointsOfInterestFile	readPointsOfInterestFile
readPointsOfInterestFile,character-method	readPointsOfInterestFile
readsToFragments	readsToFragments
readsToFragments,Data4Cseq,character-method	readsToFragments
simulateDigestion	simulateDigestion
simulateDigestion,character,character,BSgenome-method	simulateDigestion
simulateDigestion,character,character,character-method	simulateDigestion
viewpointChromosome	Data4Cseq-class
viewpointChromosome,Data4Cseq-method	Data4Cseq-class
viewpointChromosome<-	Data4Cseq-class
viewpointChromosome<-,Data4Cseq,character-method	Data4Cseq-class
viewpointInterval	Data4Cseq-class
viewpointInterval,Data4Cseq-method	Data4Cseq-class
viewpointInterval<-	Data4Cseq-class
viewpointInterval<-,Data4Cseq,numeric-method	Data4Cseq-class
visualizeViewpoint	visualizeViewpoint
visualizeViewpoint,data.frame-method	visualizeViewpoint
visualizeViewpoint,Data4Cseq-method	visualizeViewpoint
