ChIPanalyser: Predicting Transcription Factor Binding Sites
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Documentation for package ‘ChIPanalyser’ version 1.22.0
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A B C D E G I L M N P R S T W misc
-- A --
| Access | ChIPanalyserData |
| averageExpPWMScore | Accessor for 'averageExpPWMScore' slot in a 'genomicProfiles' object. |
| averageExpPWMScore-method | Class '"genomicProfilesInternal"' |
| averageExpPWMScore-methods | ~~ Methods for Function 'averageExpPWMScore' ~~ |
-- B --
| backgroundSignal | Accessor method for the 'backgroundSignal' slot in a 'parameterOptions' object. |
| backgroundSignal-method | Class '"parameterOptions"' |
| backgroundSignal-methods | ~~ Methods for Function 'backgroundSignal' ~~ |
| backgroundSignal<- | Setter method for 'backgroundSignal' slot in a 'parameterOptions' |
| backgroundSignal<--method | Class '"parameterOptions"' |
| backgroundSignal<--methods | ~~ Methods for Function 'backgroundSignal<-' ~~ |
| boundMolecules | Accessor methods for 'boundMolecules' slot in 'parameterOptions' object. |
| boundMolecules-method | Class '"parameterOptions"' |
| boundMolecules-methods | ~~ Methods for Function 'boundMolecules' ~~ |
| boundMolecules<- | Setter method for the 'boundMolecules' slot in a 'parameterOptions' object. |
| boundMolecules<--method | Class '"parameterOptions"' |
| boundMolecules<--methods | ~~ Methods for Function 'boundMolecules<-' ~~ |
| BPFrequency | Accessor method for 'BPFrequency' slot in a 'genomicProfiles' object. |
| BPFrequency-method | Class '"genomicProfilesInternal"' |
| BPFrequency-methods | ~~ Methods for Function 'BPFrequency' ~~ |
| BPFrequency<- | Setter method for 'BPFrequency' slot in a 'genomicProfiles' object. |
| BPFrequency<--method | Class '"genomicProfilesInternal"' |
| BPFrequency<--methods | ~~ Methods for Function 'BPFrequency<-' ~~ |
-- C --
| chip | ChIPanalyserData |
| ChIPanalyser | ChIPanalyser: Predicting Transcription Factor Binding Sites |
| ChIPanalyserData | ChIPanalyserData |
| chipMean | Accessor method for 'chipMean' slot in a 'parameterOptions' object. |
| chipMean-method | Class '"parameterOptions"' |
| chipMean-methods | ~~ Methods for Function 'chipMean' ~~ |
| chipMean<- | Access methods for 'chipMean' slot in 'parameterOptions' object. |
| chipMean<--method | Class '"parameterOptions"' |
| chipMean<--methods | ~~ Methods for Function 'chipMean<-' ~~ |
| ChIPScore-class | Class '"ChIPScore"' |
| chipSd | Accessor method for 'chipSd' slot in a 'parameterOptions' object. |
| chipSd-method | Class '"parameterOptions"' |
| chipSd-methods | ~~ Methods for Function 'chipSd' ~~ |
| chipSd<- | Setter methods for 'chipSd' slot in a 'parameterOptions' object. |
| chipSd<--method | Class '"parameterOptions"' |
| chipSd<--methods | ~~ Methods for Function 'chipSd<-' ~~ |
| chipSmooth | Accessor methods for 'chipSmooth' slot in a 'parameterOptions' object. |
| chipSmooth-method | Class '"parameterOptions"' |
| chipSmooth-methods | ~~ Methods for Function 'chipSmooth' ~~ |
| chipSmooth<- | Setter method for 'chipSmooth' slot in 'parameterOptions' object. |
| chipSmooth<--method | Class '"parameterOptions"' |
| 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. |
| cs | ChIPanalyserData |
-- D --
| DNASequenceLength | Accessor method for 'DNASequenceLength' slot in a 'genomicProfiles' |
| DNASequenceLength-method | Class '"genomicProfilesInternal"' |
| DNASequenceLength-methods | ~~ Methods for Function 'DNASequenceLength' ~~ |
| drop | Accessor Method for the 'drop' slot in a 'genomicProfiles' object. |
| drop-method | Class '"genomicProfilesInternal"' |
| drop-methods | ~~ Methods for Function 'drop' ~~ |
-- E --
| evolve | Running the ChIPanalyser implementation of a Genetic algorithm. |
-- G --
| generateStartingPopulation | Generate Starting population for ChIPanalyser Genetic algortihm |
| geneRef | ChIPanalyserData |
| 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 |
| GRList-class | Class '"GRList"' |
-- I --
| initialize-method | ~~ Methods for Function 'initialize' ~~ |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
-- L --
| lambdaPWM | Accessor Method for the 'lambdaPWM' slot in a 'parameterOptions' object |
| lambdaPWM-method | Class '"parameterOptions"' |
| lambdaPWM-methods | ~~ Methods for Function 'lambdaPWM' ~~ |
| lambdaPWM<- | Setter Method for the 'lambdaPWM' slot in a 'parameterOptions' object |
| lambdaPWM<--method | Class '"parameterOptions"' |
| lambdaPWM<--methods | ~~ Methods for Function 'lambdaPWM<-' ~~ |
| loci | Accessor Method for the 'loci' slot in a 'ChIPScore' object |
| loci-class | Class '"loci"' |
| loci-method | Class '"ChIPScore"' |
| loci-methods | ~~ Methods for Function 'loci' ~~ |
| lociWidth | Accessor Method for the 'lociWidth' slot in a 'parameterOptions' object |
| lociWidth-method | Class '"parameterOptions"' |
| lociWidth-methods | ~~ Methods for Function 'lociWidth' ~~ |
| lociWidth<- | Setter Method for the 'lociWidth' slot in a 'parameterOptions' object |
| lociWidth<--method | Class '"parameterOptions"' |
| lociWidth<--methods | ~~ Methods for Function 'lociWidth<-' ~~ |
-- M --
| maxPWMScore | Accessor function for 'maxPWMScore' slot in a 'genomicProfiles' object. |
| maxPWMScore-method | Class '"genomicProfilesInternal"' |
| maxPWMScore-methods | ~~ Methods for Function 'maxPWMScore' ~~ |
| maxSignal | Accessor method for the 'maxSignal' slot in a 'parameterOptions' object. |
| maxSignal-method | Class '"parameterOptions"' |
| maxSignal-methods | ~~ Methods for Function 'maxSignal' ~~ |
| maxSignal<- | Setter method for 'maxSignal' slot in a 'parameterOptions' object. |
| maxSignal<--method | Class '"parameterOptions"' |
| maxSignal<--methods | ~~ Methods for Function 'maxSignal<-' ~~ |
| minPWMScore | Accessor method the 'minPWMScore' slot in a 'genomicProfiles' object |
| minPWMScore-method | Class '"genomicProfilesInternal"' |
| minPWMScore-methods | ~~ Methods for Function 'minPWMScore' ~~ |
-- N --
| naturalLog | Accessor method the 'naturalLog' slot in a 'parameterOptions' object. |
| naturalLog-method | Class '"parameterOptions"' |
| naturalLog-methods | ~~ Methods for Function 'naturalLog' ~~ |
| naturalLog<- | Setter method for the 'naturalLog' slot in a 'parameterOptions' object. |
| naturalLog<--method | Class '"parameterOptions"' |
| naturalLog<--methods | ~~ Methods for Function 'naturalLog<-' ~~ |
| noiseFilter | Accessor Method for the 'noiseFilter' slot in a 'parameterOptions' object |
| noiseFilter-method | Class '"parameterOptions"' |
| noiseFilter-methods | ~~ Methods for Function 'noiseFilter' ~~ |
| noiseFilter<- | Setter Method for the 'noiseFilter' slot in a 'parameterOptions' object |
| noiseFilter<--method | Class '"parameterOptions"' |
| noiseFilter<--methods | ~~ Methods for Function 'noiseFilter<-' ~~ |
| noOfSites | Accessor Method for the 'noOfSites' slot in a 'parameterOptions' object |
| noOfSites-method | Class '"parameterOptions"' |
| noOfSites-methods | ~~ Methods for Function 'noOfSites' ~~ |
| noOfSites<- | Setter Method for the 'noOfSites' slot in a 'parameterOptions' object. |
| noOfSites<--method | Class '"parameterOptions"' |
| noOfSites<--methods | ~~ Methods for Function 'noOfSites<-' ~~ |
| nos-class | Class '"nos"' |
-- P --
| parameterOptions | parameter Options object |
| parameterOptions-class | Class '"parameterOptions"' |
| PFMFormat | Accesor method for the 'PFMFormat' slot in a 'genomicProfiles' object |
| PFMFormat-method | Class '"genomicProfilesInternal"' |
| PFMFormat-methods | ~~ Methods for Function 'PFMFormat' ~~ |
| PFMFormat<- | Setter method for the 'PFMFormat' slot in a 'genomicProfiles' object |
| PFMFormat<--method | Class '"genomicProfilesInternal"' |
| PFMFormat<--methods | ~~ Methods for Function 'PFMFormat<-' ~~ |
| ploidy | Accessor method for the 'ploidy' slot in a 'parameterOptions' object |
| ploidy-method | Class '"parameterOptions"' |
| ploidy-methods | ~~ Methods for Function 'ploidy' ~~ |
| ploidy<- | Setter Method for the 'ploidy' slot in an 'parameterOptions' object |
| ploidy<--method | Class '"parameterOptions"' |
| ploidy<--methods | ~~ Methods for Function 'ploidy<-' ~~ |
| plotOccupancyProfile | Plot Occupancy Profiles |
| plotOptimalHeatMaps | Heat Map of optimal Parameters |
| PositionFrequencyMatrix | Accessor method for the 'PFM' slot in a 'genomicProfiles' object |
| PositionFrequencyMatrix-method | Class '"genomicProfilesInternal"' |
| PositionFrequencyMatrix-methods | ~~ Methods for Function 'PositionFrequencyMatrix' ~~ |
| PositionFrequencyMatrix<- | Setter method for the 'PFM' slot in a 'genomicProfiles' object |
| PositionFrequencyMatrix<--method | Class '"genomicProfilesInternal"' |
| PositionFrequencyMatrix<--methods | ~~ Methods for Function 'PositionFrequencyMatrix<-' ~~ |
| PositionWeightMatrix | Accessor Method for the 'PWM' slot in a 'genomicProfiles' object |
| PositionWeightMatrix-method | Class '"genomicProfilesInternal"' |
| PositionWeightMatrix-methods | ~~ Methods for Function 'PositionWeightMatrix' ~~ |
| PositionWeightMatrix<- | Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfiles' object |
| PositionWeightMatrix<--method | Class '"genomicProfilesInternal"' |
| PositionWeightMatrix<--methods | ~~ Methods for Function 'PositionWeightMatrix<-' ~~ |
| processingChIP | Pre-processing ChIP-seq data |
| profileAccuracyEstimate | Estimating Accuracy of predicted Profiles |
| profiles | ~~ Methods for Function 'profiles' ~~ |
| profiles-method | Class '"genomicProfilesInternal"' |
| PWMpseudocount | Accessor Method for a 'PWMpseudocount' slot in a 'parameterOptions' |
| PWMpseudocount-method | Class '"parameterOptions"' |
| PWMpseudocount-methods | ~~ Methods for Function 'PWMpseudocount' ~~ |
| PWMpseudocount<- | Setter Method for the 'pseudocount' slot in a 'parameterOptions' object |
| PWMpseudocount<--method | Class '"parameterOptions"' |
| PWMpseudocount<--methods | ~~ Methods for Function 'PWMpseudocount<-' ~~ |
| PWMThreshold | Accessor method for the 'PWMThreshold' slot in a 'parameterOptions' object |
| PWMThreshold-method | Class '"parameterOptions"' |
| PWMThreshold-methods | ~~ Methods for Function 'PWMThreshold' ~~ |
| PWMThreshold<- | Setter Method for the 'PWMThreshold' slot in a 'parameterOptions' object |
| PWMThreshold<--method | Class '"parameterOptions"' |
| PWMThreshold<--methods | ~~ Methods for Function 'PWMThreshold<-' ~~ |
-- R --
| removeBackground | Accessor Method for the 'removeBackground' slot in a 'parameterOptions' object |
| removeBackground-method | Class '"parameterOptions"' |
| removeBackground-methods | ~~ Methods for Function 'removeBackground' ~~ |
| removeBackground<- | Setter Method for the 'removeBackground' slot in a 'parameterOptions' object |
| removeBackground<--method | Class '"parameterOptions"' |
| removeBackground<--methods | ~~ Methods for Function 'removeBackground<-' ~~ |
-- S --
| scores | Accessor Method for the 'scores' slot in a 'ChIPScore' object |
| scores-method | Class '"ChIPScore"' |
| scores-methods | ~~ Methods for Function 'scores' ~~ |
| searchSites | Searching function for Sites above threshold and predicted ChIP-seq Profiles |
| setChromatinStates | setChromatinStates |
| show-method | ~~ Methods for Function 'show' ~~ |
| 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-method | Class '"parameterOptions"' |
| stepSize-methods | ~~ Methods for Function 'stepSize' ~~ |
| stepSize<- | Setter Method for the 'stepSize' slot in a 'parameterOptions' |
| stepSize<--method | Class '"parameterOptions"' |
| stepSize<--methods | ~~ Methods for Function 'stepSize<-' ~~ |
| strandRule | Accessor Method for the 'strandRule' slot in a 'parameterOptions' object |
| strandRule-method | Class '"parameterOptions"' |
| strandRule-methods | ~~ Methods for Function 'strandRule' ~~ |
| strandRule<- | Setter method for the 'strandRule' slot in a 'parameterOptions' object. |
| strandRule<--method | Class '"parameterOptions"' |
| strandRule<--methods | ~~ Methods for Function 'strandRule<-' ~~ |
-- T --
| top | ChIPanalyserData |
-- W --
| whichstrand | Accessor method for the 'whichstrand' slot in a 'parameterOptions' object |
| whichstrand-method | Class '"parameterOptions"' |
| whichstrand-methods | ~~ Methods for Function 'whichstrand' ~~ |
| whichstrand<- | Setter method for the 'whichstrand' slot in a 'parameterOptions' object |
| whichstrand<--method | Class '"parameterOptions"' |
| whichstrand<--methods | ~~ Methods for Function 'whichstrand<-' ~~ |
-- misc --
| .averageExpPWMScore<--method | Class '"genomicProfilesInternal"' |
| .DNASequenceLength<--method | Class '"genomicProfilesInternal"' |
| .drop<--method | Class '"genomicProfilesInternal"' |
| .generatePWM-method | Class '"genomicProfilesInternal"' |
| .maxPWMScore<--method | Class '"genomicProfilesInternal"' |
| .minPWMScore<--method | Class '"genomicProfilesInternal"' |
| .paramTag-method | Class '"parameterOptions"' |
| .paramTag<--method | Class '"parameterOptions"' |
| .profiles<--method | Class '"genomicProfilesInternal"' |
| .tags-method | Class '"genomicProfilesInternal"' |
| .tags<--method | Class '"genomicProfilesInternal"' |
| .ZeroBackground-method | Class '"parameterOptions"' |
| .ZeroBackground<--method | Class '"parameterOptions"' |