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A B C D E G M N O P R S T W misc
| Access | ChIPanalyserData |
| AllSitesAboveThreshold | Accessor for 'AllSitesAboveThreshold' slot in a 'genomicProfileParameters' object. |
| AllSitesAboveThreshold-method | Class '"genomicProfileParameters"' |
| AllSitesAboveThreshold-methods | Accessor for 'AllSitesAboveThreshold' slot in a 'genomicProfileParameters' object. |
| averageExpPWMScore | Accessor for 'averageExpPWMScore' slot in a 'genomicProfileParameters' object. |
| averageExpPWMScore-method | Class '"genomicProfileParameters"' |
| averageExpPWMScore-methods | Accessor for 'averageExpPWMScore' slot in a 'genomicProfileParameters' object. |
| backgroundSignal | Accessor method for the 'backgroundSignal' slot in a 'occupancyProfileParameters' object. |
| backgroundSignal-method | Class '"occupancyProfileParameters"' |
| backgroundSignal-methods | Accessor method for the 'backgroundSignal' slot in a 'occupancyProfileParameters' object. |
| backgroundSignal<- | Setter method for 'backgroundSignal' slot in a 'occupancyProfileParameters' |
| backgroundSignal<--method | Class '"occupancyProfileParameters"' |
| backgroundSignal<--methods | Setter method for 'backgroundSignal' slot in a 'occupancyProfileParameters' |
| boundMolecules | Accessor methods for 'boundMolecules' slot in 'occupancyProfileParameters' object. |
| boundMolecules-method | Class '"occupancyProfileParameters"' |
| boundMolecules-methods | Accessor methods for 'boundMolecules' slot in 'occupancyProfileParameters' object. |
| boundMolecules<- | Setter method for the 'boundMolecules' slot in a 'occupancyProfileParameters' object. |
| boundMolecules<--method | Class '"occupancyProfileParameters"' |
| boundMolecules<--methods | Setter method for the 'boundMolecules' slot in a 'occupancyProfileParameters' object. |
| BPFrequency | Accessor method for 'BPFrequency' slot in a 'genomicProfileParameters' object. |
| BPFrequency-method | Class '"genomicProfileParameters"' |
| BPFrequency-methods | Accessor method for 'BPFrequency' slot in a 'genomicProfileParameters' object. |
| BPFrequency<- | Setter method for 'BPFrequency' slot in a 'genomicProfileParameters' object. |
| BPFrequency<--method | Class '"genomicProfileParameters"' |
| BPFrequency<--methods | Setter method for 'BPFrequency' slot in a 'genomicProfileParameters' object. |
| ChIPanalyser | ChIPanalyser: Predicting Transcription Factor Binding Sites |
| ChIPanalyserData | ChIPanalyserData |
| chipMean | Accessor method for 'chipMean' slot in a 'occupancyProfileParameters' object. |
| chipMean-method | Class '"occupancyProfileParameters"' |
| chipMean-methods | Accessor method for 'chipMean' slot in a 'occupancyProfileParameters' object. |
| chipMean<- | Access methods for 'chipMean' slot in 'occupancyProfileParameters' object. |
| chipMean<--method | Class '"occupancyProfileParameters"' |
| chipMean<--methods | Access methods for 'chipMean' slot in 'occupancyProfileParameters' object. |
| chipSd | Accessor method for 'chipSd' slot in a 'occupancyProfileParameters' object. |
| chipSd-method | Class '"occupancyProfileParameters"' |
| chipSd-methods | Accessor method for 'chipSd' slot in a 'occupancyProfileParameters' object. |
| chipSd<- | Setter methods for 'chipSd' slot in a 'occupancyProfileParameters' object. |
| chipSd<--method | Class '"occupancyProfileParameters"' |
| chipSd<--methods | Setter methods for 'chipSd' slot in a 'occupancyProfileParameters' object. |
| chipSmooth | Accessor methods for 'chipSmooth' slot in a 'occupancyProfileParameters' object. |
| chipSmooth-method | Class '"occupancyProfileParameters"' |
| chipSmooth-methods | Accessor methods for 'chipSmooth' slot in a 'occupancyProfileParameters' object. |
| chipSmooth<- | Setter method for 'chipSmooth' slot in 'occupancyProfileParameters' object. |
| chipSmooth<--method | Class '"occupancyProfileParameters"' |
| chipSmooth<--methods | Setter method for 'chipSmooth' slot in 'occupancyProfileParameters' object. |
| computeChipProfile | Computing ChIP-seq like profiles from Occupancy data. |
| computeGenomeWidePWMScore | Computing genome wide PWM scores. |
| computeOccupancy | Compute Occupancy values from PWM Scores based on model. |
| computeOptimal | compute Optimal Parameters |
| computePWMScore | Compute PWM Scores of sites above threshold. |
| DNASequenceLength | Accessor method for 'DNASequenceLength' slot in a 'genomicProfileParameters' |
| DNASequenceLength-method | Class '"genomicProfileParameters"' |
| DNASequenceLength-methods | Accessor method for 'DNASequenceLength' slot in a 'genomicProfileParameters' |
| DNASequenceLength<- | Setter Method for 'DNASequenceLength' slot in a 'genomicProfileParameters' object. |
| DNASequenceLength<--method | Class '"genomicProfileParameters"' |
| DNASequenceLength<--methods | Setter Method for 'DNASequenceLength' slot in a 'genomicProfileParameters' object. |
| eveLocus | ChIPanalyserData |
| eveLocusChip | ChIPanalyserData |
| geneRef | ChIPanalyserData |
| genomicProfileParameters | Genomic Profile Parameter Object |
| genomicProfileParameters-class | Class '"genomicProfileParameters"' |
| GRList-class | Class '"GRList"' |
| maxPWMScore | Accessor function for 'maxPWMScore' slot in a 'genomicProfileParameters' object. |
| maxPWMScore-method | Class '"genomicProfileParameters"' |
| maxPWMScore-methods | Accessor function for 'maxPWMScore' slot in a 'genomicProfileParameters' object. |
| maxSignal | Accessor method for the 'maxSignal' slot in a 'occupancyProfileParameters' object. |
| maxSignal-method | Class '"occupancyProfileParameters"' |
| maxSignal-methods | Accessor method for the 'maxSignal' slot in a 'occupancyProfileParameters' object. |
| maxSignal<- | Setter method for 'maxSignal' slot in a 'occupancyProfileParameters' object. |
| maxSignal<--method | Class '"occupancyProfileParameters"' |
| maxSignal<--methods | Setter method for 'maxSignal' slot in a 'occupancyProfileParameters' object. |
| minPWMScore | Accessor method the 'minPWMScore' slot in a 'genomicProfileParameters' object |
| minPWMScore-method | Class '"genomicProfileParameters"' |
| minPWMScore-methods | Accessor method the 'minPWMScore' slot in a 'genomicProfileParameters' object |
| naturalLog | Accessor method the 'naturalLog' slot in a 'genomicProfileParameters' object. |
| naturalLog-method | Class '"genomicProfileParameters"' |
| naturalLog-methods | Accessor method the 'naturalLog' slot in a 'genomicProfileParameters' object. |
| naturalLog<- | Setter method for the 'naturalLog' slot in a 'genomicProfileParameters' object. |
| naturalLog<--method | Class '"genomicProfileParameters"' |
| naturalLog<--methods | Setter method for the 'naturalLog' slot in a 'genomicProfileParameters' object. |
| NoAccess | Accessor Method for the 'NoAccess' slot in a 'genomicProfileParameters' object. |
| NoAccess-method | Class '"genomicProfileParameters"' |
| NoAccess-methods | Accessor Method for the 'NoAccess' slot in a 'genomicProfileParameters' object. |
| noOfSites | Accessor Method for the 'noOfSites' slot in a 'genomicProfileParameters' object |
| noOfSites-method | Class '"genomicProfileParameters"' |
| noOfSites-methods | Accessor Method for the 'noOfSites' slot in a 'genomicProfileParameters' object |
| noOfSites<- | Setter Method for the 'noOfSites' slot in a 'genomicProfileParameters' object. |
| noOfSites<--method | Class '"genomicProfileParameters"' |
| noOfSites<--methods | Setter Method for the 'noOfSites' slot in a 'genomicProfileParameters' object. |
| occupancyProfileParameters | Occupancy Profile Parameters |
| occupancyProfileParameters-class | Class '"occupancyProfileParameters"' |
| PFMFormat | Accesor method for the 'PFMFormat' slot in a 'genomicProfileParameters' object |
| PFMFormat-method | Class '"genomicProfileParameters"' |
| PFMFormat-methods | Accesor method for the 'PFMFormat' slot in a 'genomicProfileParameters' object |
| PFMFormat<- | Setter method for the 'PFMFormat' slot in a 'genomicProfileParameters' object |
| PFMFormat<--method | Class '"genomicProfileParameters"' |
| PFMFormat<--methods | Setter method for the 'PFMFormat' slot in a 'genomicProfileParameters' object |
| ploidy | Accessor method for the 'ploidy' slot in a 'occupancyProfileParameters' object |
| ploidy-method | Class '"occupancyProfileParameters"' |
| ploidy-methods | Accessor method for the 'ploidy' slot in a 'occupancyProfileParameters' object |
| ploidy<- | Setter Method for the 'ploidy' slot in an 'occupancyProfileParameters' object |
| ploidy<--method | Class '"occupancyProfileParameters"' |
| ploidy<--methods | Setter Method for the 'ploidy' slot in an 'occupancyProfileParameters' object |
| plotOccupancyProfile | Plot Occupancy Profiles |
| plotOptimalHeatMaps | Heat Map of optimal Parameters |
| PositionFrequencyMatrix | Accessor method for the 'PFM' slot in a 'genomicProfileParameters' object |
| PositionFrequencyMatrix-method | Class '"genomicProfileParameters"' |
| PositionFrequencyMatrix-methods | Accessor method for the 'PFM' slot in a 'genomicProfileParameters' object |
| PositionFrequencyMatrix<- | Setter method for the 'PFM' slot in a 'genomicProfileParameters' object |
| PositionFrequencyMatrix<--method | Class '"genomicProfileParameters"' |
| PositionFrequencyMatrix<--methods | Setter method for the 'PFM' slot in a 'genomicProfileParameters' object |
| PositionWeightMatrix | Accessor Method for the 'PWM' slot in a 'genomicProfileParameters' object |
| PositionWeightMatrix-method | Class '"genomicProfileParameters"' |
| PositionWeightMatrix-methods | Accessor Method for the 'PWM' slot in a 'genomicProfileParameters' object |
| PositionWeightMatrix<- | Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfileParameters' object |
| PositionWeightMatrix<--method | Class '"genomicProfileParameters"' |
| PositionWeightMatrix<--methods | Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfileParameters' object |
| processingChIPseq | Pre-processing ChIP-seq data from UCSC format file |
| profileAccuracyEstimate | Estimating Accuracy of predicted Profiles |
| PWMpseudocount | Accessor Method for a 'PWMpseudocount' slot in a 'genomicProfileParameters' |
| PWMpseudocount-method | Class '"genomicProfileParameters"' |
| PWMpseudocount-methods | Accessor Method for a 'PWMpseudocount' slot in a 'genomicProfileParameters' |
| PWMpseudocount<- | Setter Method for the 'pseudocount' slot in a 'genomicProfileParameters' object |
| PWMpseudocount<--method | Class '"genomicProfileParameters"' |
| PWMpseudocount<--methods | Setter Method for the 'pseudocount' slot in a 'genomicProfileParameters' object |
| PWMThreshold | Accessor method for the 'PWMThreshold' slot in a 'genomicProfileParameters' object |
| PWMThreshold-method | Class '"genomicProfileParameters"' |
| PWMThreshold-methods | Accessor method for the 'PWMThreshold' slot in a 'genomicProfileParameters' object |
| PWMThreshold<- | Setter Method for the 'PWMThreshold' slot in a 'genomicProfileParameters' object |
| PWMThreshold<--method | Class '"genomicProfileParameters"' |
| PWMThreshold<--methods | Setter Method for the 'PWMThreshold' slot in a 'genomicProfileParameters' object |
| removeBackground | Accessor Method for the 'removeBackground' slot in a 'occupancyProfileParameters' object |
| removeBackground-method | Class '"occupancyProfileParameters"' |
| removeBackground-methods | Accessor Method for the 'removeBackground' slot in a 'occupancyProfileParameters' object |
| removeBackground<- | Setter Method for the 'removeBackground' slot in a 'occupancyProfileParameters' object |
| removeBackground<--method | Class '"occupancyProfileParameters"' |
| removeBackground<--methods | Setter Method for the 'removeBackground' slot in a 'occupancyProfileParameters' object |
| ScalingFactorPWM | Accessor method for the 'lambda' slot in a 'genomicProfileParameters' object |
| ScalingFactorPWM-method | Class '"genomicProfileParameters"' |
| ScalingFactorPWM-methods | Accessor method for the 'lambda' slot in a 'genomicProfileParameters' object |
| ScalingFactorPWM<- | Setter method for the 'lambda' slot in a 'genomicProfileParameters' object |
| ScalingFactorPWM<--method | Class '"genomicProfileParameters"' |
| ScalingFactorPWM<--methods | Setter method for the 'lambda' slot in a 'genomicProfileParameters' object |
| searchSites | Searching function for Sites above threshold and predicted ChIP-seq Profiles |
| show-method | Class '"occupancyProfileParameters"' |
| stepSize | Accessor method of the 'stepSize' slot in 'occupancyProfileParameters' object |
| stepSize-method | Class '"occupancyProfileParameters"' |
| stepSize-methods | Accessor method of the 'stepSize' slot in 'occupancyProfileParameters' object |
| stepSize<- | Setter Method for the 'stepSize' slot in a 'occupancyProfileParameters' |
| stepSize<--method | Class '"occupancyProfileParameters"' |
| stepSize<--methods | Setter Method for the 'stepSize' slot in a 'occupancyProfileParameters' |
| strandRule | Accessor Method for the 'strandRule' slot in a 'genomicProfileParameters' object |
| strandRule-method | Class '"genomicProfileParameters"' |
| strandRule-methods | Accessor Method for the 'strandRule' slot in a 'genomicProfileParameters' object |
| strandRule<- | Setter method for the 'strandRule' slot in a 'genomicProfileParameters' object. |
| strandRule<--method | Class '"genomicProfileParameters"' |
| strandRule<--methods | Setter method for the 'strandRule' slot in a 'genomicProfileParameters' object. |
| thetaThreshold | Accessor method for the 'thetaThreshold' slot in a 'occupancyProfileParameters' object |
| thetaThreshold-method | Class '"occupancyProfileParameters"' |
| thetaThreshold-methods | Accessor method for the 'thetaThreshold' slot in a 'occupancyProfileParameters' object |
| thetaThreshold<- | Setter method the 'thetaThreshold' slot in a 'occupancyProfileParameters' object |
| thetaThreshold<--method | Class '"occupancyProfileParameters"' |
| thetaThreshold<--methods | Setter method the 'thetaThreshold' slot in a 'occupancyProfileParameters' object |
| whichstrand | Accessor method for the 'whichstrand' slot in a 'genomicProfileParameters' object |
| whichstrand-method | Class '"genomicProfileParameters"' |
| whichstrand-methods | Accessor method for the 'whichstrand' slot in a 'genomicProfileParameters' object |
| whichstrand<- | Setter method for the 'whichstrand' slot in a 'genomicProfileParameters' object |
| whichstrand<--method | Class '"genomicProfileParameters"' |
| whichstrand<--methods | Setter method for the 'whichstrand' slot in a 'genomicProfileParameters' object |
| .ZeroBackground-method | Class '"genomicProfileParameters"' |
| .ZeroBackground<--method | Class '"genomicProfileParameters"' |