.averageExpPWMScore<-,genomicProfilesInternal,numeric-method	genomicProfilesInternal-class
.DNASequenceLength<-,genomicProfilesInternal,vector-method	genomicProfilesInternal-class
.drop<-,genomicProfilesInternal,vector-method	genomicProfilesInternal-class
.generatePWM,genomicProfilesInternal-method	genomicProfilesInternal-class
.maxPWMScore<-,genomicProfilesInternal,vector-method	genomicProfilesInternal-class
.minPWMScore<-,genomicProfilesInternal,vector-method	genomicProfilesInternal-class
.paramTag,parameterOptions-method	parameterOptions-class
.paramTag<-,parameterOptions,character-method	parameterOptions-class
.profiles<-,genomicProfilesInternal,GRList-method	genomicProfilesInternal-class
.tags,genomicProfilesInternal-method	genomicProfilesInternal-class
.tags<-,genomicProfilesInternal,character-method	genomicProfilesInternal-class
.ZeroBackground,parameterOptions-method	parameterOptions-class
.ZeroBackground<-,parameterOptions,vector-method	parameterOptions-class
Access	data
averageExpPWMScore	averageExpPWMScore
averageExpPWMScore,genomicProfilesInternal-method	genomicProfilesInternal-class
averageExpPWMScore-methods	averageExpPWMScore-methods
backgroundSignal	backgroundSignal
backgroundSignal,parameterOptions-method	parameterOptions-class
backgroundSignal-methods	backgroundSignal-methods
backgroundSignal<-	backgroundSignal_-
backgroundSignal<-,parameterOptions,numeric-method	parameterOptions-class
backgroundSignal<--methods	backgroundSignal_--methods
boundMolecules	boundMolecules
boundMolecules,parameterOptions-method	parameterOptions-class
boundMolecules-methods	boundMolecules-methods
boundMolecules<-	boundMolecules_-
boundMolecules<-,parameterOptions,vector-method	parameterOptions-class
boundMolecules<--methods	boundMolecules_--methods
BPFrequency	BPFrequency
BPFrequency,genomicProfilesInternal-method	genomicProfilesInternal-class
BPFrequency-methods	BPFrequency-methods
BPFrequency<-	BPFrequency_-
BPFrequency<-,genomicProfilesInternal,DNAStringSet-method	genomicProfilesInternal-class
BPFrequency<-,genomicProfilesInternal,vector-method	genomicProfilesInternal-class
BPFrequency<--methods	BPFrequency_--methods
chip	data
ChIPanalyser	ChIPanalyser-package
ChIPanalyserData	data
chipMean	chipMean
chipMean,parameterOptions-method	parameterOptions-class
chipMean-methods	chipMean-methods
chipMean<-	chipMean_-
chipMean<-,parameterOptions,numeric-method	parameterOptions-class
chipMean<--methods	chipMean_--methods
ChIPScore-class	ChIPScore-class
chipSd	chipSd
chipSd,parameterOptions-method	parameterOptions-class
chipSd-methods	chipSd-methods
chipSd<-	chipSd_-
chipSd<-,parameterOptions,numeric-method	parameterOptions-class
chipSd<--methods	chipSd_--methods
chipSmooth	chipSmooth
chipSmooth,parameterOptions-method	parameterOptions-class
chipSmooth-methods	chipSmooth-methods
chipSmooth<-	chipSmooth_-
chipSmooth<-,parameterOptions,vector-method	parameterOptions-class
chipSmooth<--methods	chipSmooth_--methods
computeChIPProfile	computeChIPProfile
computeGenomeWideScores	computeGenomeWideScores
computeOccupancy	computeOccupancy
computeOptimal	computeOptimal
computePWMScore	computePWMScore
cs	data
DNASequenceLength	DNASequenceLength
DNASequenceLength,genomicProfilesInternal-method	genomicProfilesInternal-class
DNASequenceLength-methods	DNASequenceLength-methods
drop	drop
drop,genomicProfilesInternal-method	genomicProfilesInternal-class
drop-methods	drop-methods
evolve	evolve
generateStartingPopulation	generateStartingPopulation
geneRef	data
genomicProfiles	genomicProfiles
genomicProfiles-class	genomicProfiles-class
genomicProfilesInternal-class	genomicProfilesInternal-class
getHighestFitnessSolutions	getHighestFitnessSolutions
getTestingData	getTestingData
getTrainingData	getTrainingData
GRList-class	GRList-class
initialize,ChIPScore-method	initialize-methods
initialize,genomicProfiles-method	initialize-methods
initialize,parameterOptions-method	initialize-methods
initialize-methods	initialize-methods
lambdaPWM	lambdaPWM
lambdaPWM,parameterOptions-method	parameterOptions-class
lambdaPWM-methods	lambdaPWM-methods
lambdaPWM<-	lambdaPWM_
lambdaPWM<-,parameterOptions,vector-method	parameterOptions-class
lambdaPWM<--methods	lambdaPWM_--methods
loci	loci
loci,ChIPScore-method	ChIPScore-class
loci-class	loci-class
loci-methods	loci-methods
lociWidth	lociWidth
lociWidth,parameterOptions-method	parameterOptions-class
lociWidth-methods	lociWidth-methods
lociWidth<-	lociWidth_
lociWidth<-,parameterOptions,numeric-method	parameterOptions-class
lociWidth<--methods	lociWidth_--methods
maxPWMScore	maxPWMScore
maxPWMScore,genomicProfilesInternal-method	genomicProfilesInternal-class
maxPWMScore-methods	maxPWMScore-methods
maxSignal	maxSignal
maxSignal,parameterOptions-method	parameterOptions-class
maxSignal-methods	maxSignal-methods
maxSignal<-	maxSignal_-
maxSignal<-,parameterOptions,numeric-method	parameterOptions-class
maxSignal<--methods	maxSignal_--methods
minPWMScore	minPWMScore
minPWMScore,genomicProfilesInternal-method	genomicProfilesInternal-class
minPWMScore-methods	minPWMScore-methods
naturalLog	naturalLog
naturalLog,parameterOptions-method	parameterOptions-class
naturalLog-methods	naturalLog-methods
naturalLog<-	naturalLog_-
naturalLog<-,parameterOptions,logical-method	parameterOptions-class
naturalLog<--methods	naturalLog_--methods
noiseFilter	noiseFilter
noiseFilter,parameterOptions-method	parameterOptions-class
noiseFilter-methods	noiseFilter-methods
noiseFilter<-	noiseFilter_
noiseFilter<-,parameterOptions,character-method	parameterOptions-class
noiseFilter<--methods	noiseFilter_--methods
noOfSites	noOfSites
noOfSites,parameterOptions-method	parameterOptions-class
noOfSites-methods	noOfSites-methods
noOfSites<-	noOfSites_-
noOfSites<-,parameterOptions,character-method	parameterOptions-class
noOfSites<-,parameterOptions,numeric-method	parameterOptions-class
noOfSites<--methods	noOfSites_--methods
nos-class	nos-class
parameterOptions	parameterOptions
parameterOptions-class	parameterOptions-class
PFMFormat	PFMFormat
PFMFormat,genomicProfilesInternal-method	genomicProfilesInternal-class
PFMFormat-methods	PFMFormat-methods
PFMFormat<-	PFMFormat_
PFMFormat<-,genomicProfilesInternal,character-method	genomicProfilesInternal-class
PFMFormat<--methods	PFMFormat_--methods
ploidy	ploidy
ploidy,parameterOptions-method	parameterOptions-class
ploidy-methods	ploidy-methods
ploidy<-	ploidy_-
ploidy<-,parameterOptions,numeric-method	parameterOptions-class
ploidy<--methods	ploidy_--methods
plotOccupancyProfile	plotOccupancyProfile
plotOptimalHeatMaps	plotOptimalHeatMaps
PositionFrequencyMatrix	PositionFrequencyMatrix
PositionFrequencyMatrix,genomicProfilesInternal-method	genomicProfilesInternal-class
PositionFrequencyMatrix-methods	PositionFrequencyMatrix-methods
PositionFrequencyMatrix<-	PositionFrequencyMatrix_-
PositionFrequencyMatrix<-,genomicProfilesInternal,character-method	genomicProfilesInternal-class
PositionFrequencyMatrix<-,genomicProfilesInternal,matrix-method	genomicProfilesInternal-class
PositionFrequencyMatrix<--methods	PositionFrequencyMatrix_--methods
PositionWeightMatrix	PositionWeightMatrix
PositionWeightMatrix,genomicProfilesInternal-method	genomicProfilesInternal-class
PositionWeightMatrix-methods	PositionWeightMatrix-methods
PositionWeightMatrix<-	PositionWeightMatrix_-
PositionWeightMatrix<-,genomicProfilesInternal,matrix-method	genomicProfilesInternal-class
PositionWeightMatrix<--methods	PositionWeightMatrix_--methods
processingChIP	processingChIP
profileAccuracyEstimate	profileAccuracyEstimate
profiles	profiles-methods
profiles,genomicProfilesInternal-method	genomicProfilesInternal-class
PWMpseudocount	PWMpseudocount
PWMpseudocount,parameterOptions-method	parameterOptions-class
PWMpseudocount-methods	PWMpseudocount-methods
PWMpseudocount<-	PWMpseudocount_-
PWMpseudocount<-,parameterOptions,numeric-method	parameterOptions-class
PWMpseudocount<--methods	PWMpseudocount_--methods
PWMThreshold	PWMThreshold
PWMThreshold,parameterOptions-method	parameterOptions-class
PWMThreshold-methods	PWMThreshold-methods
PWMThreshold<-	PWMThreshold_-
PWMThreshold<-,parameterOptions,numeric-method	parameterOptions-class
PWMThreshold<--methods	PWMThreshold_--methods
removeBackground	removeBackground
removeBackground,parameterOptions-method	parameterOptions-class
removeBackground-methods	removeBackground-methods
removeBackground<-	removeBackground_-
removeBackground<-,parameterOptions,vector-method	parameterOptions-class
removeBackground<--methods	removeBackground_--methods
scores	scores
scores,ChIPScore-method	ChIPScore-class
scores-methods	scores-methods
searchSites	searchSites
setChromatinStates	setChromatinStates
show,ChIPScore-method	show-methods
show,genomicProfiles-method	show-methods
show,parameterOptions-method	show-methods
show-methods	show-methods
singleRun	singleRun
splitData	splitData
stepSize	stepSize
stepSize,parameterOptions-method	parameterOptions-class
stepSize-methods	stepSize-methods
stepSize<-	stepSize_-
stepSize<-,parameterOptions,numeric-method	parameterOptions-class
stepSize<--methods	stepSize_--methods
strandRule	strandRule
strandRule,parameterOptions-method	parameterOptions-class
strandRule-methods	strandRule-methods
strandRule<-	strandRule_-
strandRule<-,parameterOptions,character-method	parameterOptions-class
strandRule<--methods	strandRule_--methods
top	data
whichstrand	whichstrand
whichstrand,parameterOptions-method	parameterOptions-class
whichstrand-methods	whichstrand-methods
whichstrand<-	whichstrand_-
whichstrand<-,parameterOptions,character-method	parameterOptions-class
whichstrand<--methods	whichstrand_--methods
