.ZeroBackground,genomicProfileParameters-method	genomicProfileParameters-class
.ZeroBackground<-,genomicProfileParameters,vector-method	genomicProfileParameters-class
Access	data
AllSitesAboveThreshold	AllSitesAboveThreshold
AllSitesAboveThreshold,genomicProfileParameters-method	genomicProfileParameters-class
AllSitesAboveThreshold-methods	AllSitesAboveThreshold
averageExpPWMScore	averageExpPWMScore
averageExpPWMScore,genomicProfileParameters-method	genomicProfileParameters-class
averageExpPWMScore-methods	averageExpPWMScore
backgroundSignal	backgroundSignal
backgroundSignal,occupancyProfileParameters-method	occupancyProfileParameters-class
backgroundSignal-methods	backgroundSignal
backgroundSignal<-	backgroundSignal_-
backgroundSignal<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
backgroundSignal<--methods	backgroundSignal_-
boundMolecules	boundMolecules
boundMolecules,occupancyProfileParameters-method	occupancyProfileParameters-class
boundMolecules-methods	boundMolecules
boundMolecules<-	boundMolecules_-
boundMolecules<-,occupancyProfileParameters,vector-method	occupancyProfileParameters-class
boundMolecules<--methods	boundMolecules_-
BPFrequency	BPFrequency
BPFrequency,genomicProfileParameters-method	genomicProfileParameters-class
BPFrequency-methods	BPFrequency
BPFrequency<-	BPFrequency_-
BPFrequency<-,genomicProfileParameters,DNAStringSet-method	genomicProfileParameters-class
BPFrequency<-,genomicProfileParameters,vector-method	genomicProfileParameters-class
BPFrequency<--methods	BPFrequency_-
ChIPanalyser	ChIPanalyser-package
ChIPanalyserData	data
chipMean	chipMean
chipMean,occupancyProfileParameters-method	occupancyProfileParameters-class
chipMean-methods	chipMean
chipMean<-	chipMean_-
chipMean<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
chipMean<--methods	chipMean_-
chipSd	chipSd
chipSd,occupancyProfileParameters-method	occupancyProfileParameters-class
chipSd-methods	chipSd
chipSd<-	chipSd_-
chipSd<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
chipSd<--methods	chipSd_-
chipSmooth	chipSmooth
chipSmooth,occupancyProfileParameters-method	occupancyProfileParameters-class
chipSmooth-methods	chipSmooth
chipSmooth<-	chipSmooth_-
chipSmooth<-,occupancyProfileParameters,vector-method	occupancyProfileParameters-class
chipSmooth<--methods	chipSmooth_-
computeChipProfile	computeChipProfile
computeGenomeWidePWMScore	computeGenomeWidePWMScore
computeOccupancy	computeOccupancy
computeOptimal	computeOptimal
computePWMScore	computePWMScore
DNASequenceLength	DNASequenceLength
DNASequenceLength,genomicProfileParameters-method	genomicProfileParameters-class
DNASequenceLength-methods	DNASequenceLength
DNASequenceLength<-	DNASequenceLength_-
DNASequenceLength<-,genomicProfileParameters,vector-method	genomicProfileParameters-class
DNASequenceLength<--methods	DNASequenceLength_-
eveLocus	data
eveLocusChip	data
geneRef	data
genomicProfileParameters	genomicProfileParameters
genomicProfileParameters-class	genomicProfileParameters-class
GRList-class	GRList-class
maxPWMScore	maxPWMScore
maxPWMScore,genomicProfileParameters-method	genomicProfileParameters-class
maxPWMScore-methods	maxPWMScore
maxSignal	maxSignal
maxSignal,occupancyProfileParameters-method	occupancyProfileParameters-class
maxSignal-methods	maxSignal
maxSignal<-	maxSignal_-
maxSignal<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
maxSignal<--methods	maxSignal_-
minPWMScore	minPWMScore
minPWMScore,genomicProfileParameters-method	genomicProfileParameters-class
minPWMScore-methods	minPWMScore
naturalLog	naturalLog
naturalLog,genomicProfileParameters-method	genomicProfileParameters-class
naturalLog-methods	naturalLog
naturalLog<-	naturalLog_-
naturalLog<-,genomicProfileParameters,logical-method	genomicProfileParameters-class
naturalLog<--methods	naturalLog_-
NoAccess	NoAccess
NoAccess,genomicProfileParameters-method	genomicProfileParameters-class
NoAccess-methods	NoAccess
noOfSites	noOfSites
noOfSites,genomicProfileParameters-method	genomicProfileParameters-class
noOfSites-methods	noOfSites
noOfSites<-	noOfSites_-
noOfSites<-,genomicProfileParameters,vector-method	genomicProfileParameters-class
noOfSites<--methods	noOfSites_-
occupancyProfileParameters	occupancyProfileParameters
occupancyProfileParameters-class	occupancyProfileParameters-class
PFMFormat	PFMFormat
PFMFormat,genomicProfileParameters-method	genomicProfileParameters-class
PFMFormat-methods	PFMFormat
PFMFormat<-	PFMFormat_
PFMFormat<-,genomicProfileParameters,character-method	genomicProfileParameters-class
PFMFormat<--methods	PFMFormat_
ploidy	ploidy
ploidy,occupancyProfileParameters-method	occupancyProfileParameters-class
ploidy-methods	ploidy
ploidy<-	ploidy_-
ploidy<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
ploidy<--methods	ploidy_-
plotOccupancyProfile	plotOccupancyProfile
plotOptimalHeatMaps	plotOptimalHeatMaps
PositionFrequencyMatrix	PositionFrequencyMatrix
PositionFrequencyMatrix,genomicProfileParameters-method	genomicProfileParameters-class
PositionFrequencyMatrix-methods	PositionFrequencyMatrix
PositionFrequencyMatrix<-	PositionFrequencyMatrix_-
PositionFrequencyMatrix<-,genomicProfileParameters,character-method	genomicProfileParameters-class
PositionFrequencyMatrix<-,genomicProfileParameters,matrix-method	genomicProfileParameters-class
PositionFrequencyMatrix<--methods	PositionFrequencyMatrix_-
PositionWeightMatrix	PositionWeightMatrix
PositionWeightMatrix,genomicProfileParameters-method	genomicProfileParameters-class
PositionWeightMatrix-methods	PositionWeightMatrix
PositionWeightMatrix<-	PositionWeightMatrix_-
PositionWeightMatrix<-,genomicProfileParameters,matrix-method	genomicProfileParameters-class
PositionWeightMatrix<--methods	PositionWeightMatrix_-
processingChIPseq	processingChIPseq
profileAccuracyEstimate	profileAccuracyEstimate
PWMpseudocount	PWMpseudocount
PWMpseudocount,genomicProfileParameters-method	genomicProfileParameters-class
PWMpseudocount-methods	PWMpseudocount
PWMpseudocount<-	PWMpseudocount_-
PWMpseudocount<-,genomicProfileParameters,numeric-method	genomicProfileParameters-class
PWMpseudocount<--methods	PWMpseudocount_-
PWMThreshold	PWMThreshold
PWMThreshold,genomicProfileParameters-method	genomicProfileParameters-class
PWMThreshold-methods	PWMThreshold
PWMThreshold<-	PWMThreshold_-
PWMThreshold<-,genomicProfileParameters,numeric-method	genomicProfileParameters-class
PWMThreshold<--methods	PWMThreshold_-
removeBackground	removeBackground
removeBackground,occupancyProfileParameters-method	occupancyProfileParameters-class
removeBackground-methods	removeBackground
removeBackground<-	removeBackground_-
removeBackground<-,occupancyProfileParameters,vector-method	occupancyProfileParameters-class
removeBackground<--methods	removeBackground_-
ScalingFactorPWM	ScalingFactorPWM
ScalingFactorPWM,genomicProfileParameters-method	genomicProfileParameters-class
ScalingFactorPWM-methods	ScalingFactorPWM
ScalingFactorPWM<-	ScalingFactorPWM_-
ScalingFactorPWM<-,genomicProfileParameters,vector-method	genomicProfileParameters-class
ScalingFactorPWM<--methods	ScalingFactorPWM_-
searchSites	searchSites
show,occupancyProfileParameters-method	occupancyProfileParameters-class
stepSize	stepSize
stepSize,occupancyProfileParameters-method	occupancyProfileParameters-class
stepSize-methods	stepSize
stepSize<-	stepSize_-
stepSize<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
stepSize<--methods	stepSize_-
strandRule	strandRule
strandRule,genomicProfileParameters-method	genomicProfileParameters-class
strandRule-methods	strandRule
strandRule<-	strandRule_-
strandRule<-,genomicProfileParameters,character-method	genomicProfileParameters-class
strandRule<--methods	strandRule_-
thetaThreshold,occupancyProfileParameters-method	occupancyProfileParameters-class
thetaThreshold<-,occupancyProfileParameters,numeric-method	occupancyProfileParameters-class
whichstrand	whichstrand
whichstrand,genomicProfileParameters-method	genomicProfileParameters-class
whichstrand-methods	whichstrand
whichstrand<-	whichstrand_-
whichstrand<-,genomicProfileParameters,character-method	genomicProfileParameters-class
whichstrand<--methods	whichstrand_-
