BPFrequency             Accessor method for 'BPFrequency' slot in a
                        'genomicProfiles' object.
BPFrequency-methods     ~~ Methods for Function 'BPFrequency' ~~
BPFrequency<-           Setter method for 'BPFrequency' slot in a
                        'genomicProfiles' object.
BPFrequency<--methods   ~~ Methods for Function 'BPFrequency<-' ~~
ChIPScore-class         Class '"ChIPScore"'
ChIPanalyser            ChIPanalyser: Predicting Transcription Factor
                        Binding Sites
ChIPanalyserData        ChIPanalyserData
DNASequenceLength       Accessor method for 'DNASequenceLength' slot in
                        a 'genomicProfiles'
DNASequenceLength-methods
                        ~~ Methods for Function 'DNASequenceLength' ~~
GRList-class            Class '"GRList"'
PFMFormat               Accesor method for the 'PFMFormat' slot in a
                        'genomicProfiles' object
PFMFormat-methods       ~~ Methods for Function 'PFMFormat' ~~
PFMFormat<-             Setter method for the 'PFMFormat' slot in a
                        'genomicProfiles' object
PFMFormat<--methods     ~~ Methods for Function 'PFMFormat<-' ~~
PWMThreshold            Accessor method for the 'PWMThreshold' slot in
                        a 'parameterOptions' object
PWMThreshold-methods    ~~ Methods for Function 'PWMThreshold' ~~
PWMThreshold<-          Setter Method for the 'PWMThreshold' slot in a
                        'parameterOptions' object
PWMThreshold<--methods
                        ~~ Methods for Function 'PWMThreshold<-' ~~
PWMpseudocount          Accessor Method for a 'PWMpseudocount' slot in
                        a 'parameterOptions'
PWMpseudocount-methods
                        ~~ Methods for Function 'PWMpseudocount' ~~
PWMpseudocount<-        Setter Method for the 'pseudocount' slot in a
                        'parameterOptions' object
PWMpseudocount<--methods
                        ~~ Methods for Function 'PWMpseudocount<-' ~~
PositionFrequencyMatrix
                        Accessor method for the 'PFM' slot in a
                        'genomicProfiles' object
PositionFrequencyMatrix-methods
                        ~~ Methods for Function
                        'PositionFrequencyMatrix' ~~
PositionFrequencyMatrix<-
                        Setter method for the 'PFM' slot in a
                        'genomicProfiles' object
PositionFrequencyMatrix<--methods
                        ~~ Methods for Function
                        'PositionFrequencyMatrix<-' ~~
PositionWeightMatrix    Accessor Method for the 'PWM' slot in a
                        'genomicProfiles' object
PositionWeightMatrix-methods
                        ~~ Methods for Function 'PositionWeightMatrix'
                        ~~
PositionWeightMatrix<-
                        Setter Method for the 'PositionWeightMatrix'
                        slot in a 'genomicProfiles' object
PositionWeightMatrix<--methods
                        ~~ Methods for Function
                        'PositionWeightMatrix<-' ~~
averageExpPWMScore      Accessor for 'averageExpPWMScore' slot in a
                        'genomicProfiles' object.
averageExpPWMScore-methods
                        ~~ Methods for Function 'averageExpPWMScore' ~~
backgroundSignal        Accessor method for the 'backgroundSignal' slot
                        in a 'parameterOptions' object.
backgroundSignal-methods
                        ~~ Methods for Function 'backgroundSignal' ~~
backgroundSignal<-      Setter method for 'backgroundSignal' slot in a
                        'parameterOptions'
backgroundSignal<--methods
                        ~~ Methods for Function 'backgroundSignal<-' ~~
boundMolecules          Accessor methods for 'boundMolecules' slot in
                        'parameterOptions' object.
boundMolecules-methods
                        ~~ Methods for Function 'boundMolecules' ~~
boundMolecules<-        Setter method for the 'boundMolecules' slot in
                        a 'parameterOptions' object.
boundMolecules<--methods
                        ~~ Methods for Function 'boundMolecules<-' ~~
chipMean                Accessor method for 'chipMean' slot in a
                        'parameterOptions' object.
chipMean-methods        ~~ Methods for Function 'chipMean' ~~
chipMean<-              Access methods for 'chipMean' slot in
                        'parameterOptions' object.
chipMean<--methods      ~~ Methods for Function 'chipMean<-' ~~
chipSd                  Accessor method for 'chipSd' slot in a
                        'parameterOptions' object.
chipSd-methods          ~~ Methods for Function 'chipSd' ~~
chipSd<-                Setter methods for 'chipSd' slot in a
                        'parameterOptions' object.
chipSd<--methods        ~~ Methods for Function 'chipSd<-' ~~
chipSmooth              Accessor methods for 'chipSmooth' slot in a
                        'parameterOptions' object.
chipSmooth-methods      ~~ Methods for Function 'chipSmooth' ~~
chipSmooth<-            Setter method for 'chipSmooth' slot in
                        'parameterOptions' object.
chipSmooth<--methods    ~~ Methods for Function 'chipSmooth<-' ~~
computeChIPProfile      Computing ChIP-seq like profiles from Occupancy
                        data.
computeGenomeWideScores
                        Computing Genome Wide scores
computeOccupancy        Compute Occupancy values from PWM Scores based
                        on model.
computeOptimal          compute Optimal Parameters
computePWMScore         Compute PWM Scores of sites above threshold.
drop                    Accessor Method for the 'drop' slot in a
                        'genomicProfiles' object.
drop-methods            ~~ Methods for Function 'drop' ~~
evolve                  Running the ChIPanalyser implementation of a
                        Genetic algorithm.
generateStartingPopulation
                        Generate Starting population for ChIPanalyser
                        Genetic algortihm
genomicProfiles         Genomic Profile object
genomicProfiles-class   Class '"genomicProfiles"'
genomicProfilesInternal-class
                        Class '"genomicProfilesInternal"'
getHighestFitnessSolutions
                        Get Highest Fitness Solutions
getTestingData          Extract testing data from ChIPscore object
getTrainingData         Extract training data from ChIPscore object
initialize-methods      ~~ Methods for Function 'initialize' ~~
lambdaPWM               Accessor Method for the 'lambdaPWM' slot in a
                        'parameterOptions' object
lambdaPWM-methods       ~~ Methods for Function 'lambdaPWM' ~~
lambdaPWM<-             Setter Method for the 'lambdaPWM' slot in a
                        'parameterOptions' object
lambdaPWM<--methods     ~~ Methods for Function 'lambdaPWM<-' ~~
loci                    Accessor Method for the 'loci' slot in a
                        'ChIPScore' object
loci-class              Class '"loci"'
loci-methods            ~~ Methods for Function 'loci' ~~
lociWidth               Accessor Method for the 'lociWidth' slot in a
                        'parameterOptions' object
lociWidth-methods       ~~ Methods for Function 'lociWidth' ~~
lociWidth<-             Setter Method for the 'lociWidth' slot in a
                        'parameterOptions' object
lociWidth<--methods     ~~ Methods for Function 'lociWidth<-' ~~
maxPWMScore             Accessor function for 'maxPWMScore' slot in a
                        'genomicProfiles' object.
maxPWMScore-methods     ~~ Methods for Function 'maxPWMScore' ~~
maxSignal               Accessor method for the 'maxSignal' slot in a
                        'parameterOptions' object.
maxSignal-methods       ~~ Methods for Function 'maxSignal' ~~
maxSignal<-             Setter method for 'maxSignal' slot in a
                        'parameterOptions' object.
maxSignal<--methods     ~~ Methods for Function 'maxSignal<-' ~~
minPWMScore             Accessor method the 'minPWMScore' slot in a
                        'genomicProfiles' object
minPWMScore-methods     ~~ Methods for Function 'minPWMScore' ~~
naturalLog              Accessor method the 'naturalLog' slot in a
                        'parameterOptions' object.
naturalLog-methods      ~~ Methods for Function 'naturalLog' ~~
naturalLog<-            Setter method for the 'naturalLog' slot in a
                        'parameterOptions' object.
naturalLog<--methods    ~~ Methods for Function 'naturalLog<-' ~~
noOfSites               Accessor Method for the 'noOfSites' slot in a
                        'parameterOptions' object
noOfSites-methods       ~~ Methods for Function 'noOfSites' ~~
noOfSites<-             Setter Method for the 'noOfSites' slot in a
                        'parameterOptions' object.
noOfSites<--methods     ~~ Methods for Function 'noOfSites<-' ~~
noiseFilter             Accessor Method for the 'noiseFilter' slot in a
                        'parameterOptions' object
noiseFilter-methods     ~~ Methods for Function 'noiseFilter' ~~
noiseFilter<-           Setter Method for the 'noiseFilter' slot in a
                        'parameterOptions' object
noiseFilter<--methods   ~~ Methods for Function 'noiseFilter<-' ~~
nos-class               Class '"nos"'
parameterOptions        parameter Options object
parameterOptions-class
                        Class '"parameterOptions"'
ploidy                  Accessor method for the 'ploidy' slot in a
                        'parameterOptions' object
ploidy-methods          ~~ Methods for Function 'ploidy' ~~
ploidy<-                Setter Method for the 'ploidy' slot in an
                        'parameterOptions' object
ploidy<--methods        ~~ Methods for Function 'ploidy<-' ~~
plotOccupancyProfile    Plot Occupancy Profiles
plotOptimalHeatMaps     Heat Map of optimal Parameters
processingChIP          Pre-processing ChIP-seq data
profileAccuracyEstimate
                        Estimating Accuracy of predicted Profiles
profiles                ~~ Methods for Function 'profiles' ~~
removeBackground        Accessor Method for the 'removeBackground' slot
                        in a 'parameterOptions' object
removeBackground-methods
                        ~~ Methods for Function 'removeBackground' ~~
removeBackground<-      Setter Method for the 'removeBackground' slot
                        in a 'parameterOptions' object
removeBackground<--methods
                        ~~ Methods for Function 'removeBackground<-' ~~
scores                  Accessor Method for the 'scores' slot in a
                        'ChIPScore' object
scores-methods          ~~ Methods for Function 'scores' ~~
searchSites             Searching function for Sites above threshold
                        and predicted ChIP-seq Profiles
setChromatinStates      setChromatinStates
show-methods            ~~ Methods for Function 'show' ~~
singleRun               singleRun
splitData               Get Training and Testing data from ChIPscore
                        objects
stepSize                Accessor method of the 'stepSize' slot in
                        'parameterOptions' object
stepSize-methods        ~~ Methods for Function 'stepSize' ~~
stepSize<-              Setter Method for the 'stepSize' slot in a
                        'parameterOptions'
stepSize<--methods      ~~ Methods for Function 'stepSize<-' ~~
strandRule              Accessor Method for the 'strandRule' slot in a
                        'parameterOptions' object
strandRule-methods      ~~ Methods for Function 'strandRule' ~~
strandRule<-            Setter method for the 'strandRule' slot in a
                        'parameterOptions' object.
strandRule<--methods    ~~ Methods for Function 'strandRule<-' ~~
whichstrand             Accessor method for the 'whichstrand' slot in a
                        'parameterOptions' object
whichstrand-methods     ~~ Methods for Function 'whichstrand' ~~
whichstrand<-           Setter method for the 'whichstrand' slot in a
                        'parameterOptions' object
whichstrand<--methods   ~~ Methods for Function 'whichstrand<-' ~~
