Man pages for patrickCNMartin/ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding Sites
| averageExpPWMScore | Accessor for 'averageExpPWMScore' slot in a 'genomicProfiles'... |
| averageExpPWMScore-methods | ~~ Methods for Function 'averageExpPWMScore' ~~ |
| backgroundSignal | Accessor method for the 'backgroundSignal' slot in a... |
| backgroundSignal_- | Setter method for 'backgroundSignal' slot in a... |
| backgroundSignal_--methods | ~~ Methods for Function 'backgroundSignal<-' ~~ |
| backgroundSignal-methods | ~~ Methods for Function 'backgroundSignal' ~~ |
| boundMolecules | Accessor methods for 'boundMolecules' slot in... |
| boundMolecules_- | Setter method for the 'boundMolecules' slot in a... |
| boundMolecules_--methods | ~~ Methods for Function 'boundMolecules<-' ~~ |
| boundMolecules-methods | ~~ Methods for Function 'boundMolecules' ~~ |
| BPFrequency | Accessor method for 'BPFrequency' slot in a 'genomicProfiles'... |
| BPFrequency_- | Setter method for 'BPFrequency' slot in a 'genomicProfiles'... |
| BPFrequency_--methods | ~~ Methods for Function 'BPFrequency<-' ~~ |
| BPFrequency-methods | ~~ Methods for Function 'BPFrequency' ~~ |
| ChIPanalyser-package | ChIPanalyser: Predicting Transcription Factor Binding Sites |
| chipMean | Accessor method for 'chipMean' slot in a 'parameterOptions'... |
| chipMean_- | Access methods for 'chipMean' slot in 'parameterOptions'... |
| chipMean_--methods | ~~ Methods for Function 'chipMean<-' ~~ |
| chipMean-methods | ~~ Methods for Function 'chipMean' ~~ |
| ChIPScore-class | Class '"ChIPScore"' |
| chipSd | Accessor method for 'chipSd' slot in a 'parameterOptions'... |
| chipSd_- | Setter methods for 'chipSd' slot in a 'parameterOptions'... |
| chipSd_--methods | ~~ Methods for Function 'chipSd<-' ~~ |
| chipSd-methods | ~~ Methods for Function 'chipSd' ~~ |
| chipSmooth | Accessor methods for 'chipSmooth' slot in a... |
| chipSmooth_- | Setter method for 'chipSmooth' slot in 'parameterOptions'... |
| chipSmooth_--methods | ~~ Methods for Function 'chipSmooth<-' ~~ |
| 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. |
| data | ChIPanalyserData |
| DNASequenceLength | Accessor method for 'DNASequenceLength' slot in a... |
| DNASequenceLength-methods | ~~ Methods for Function 'DNASequenceLength' ~~ |
| drop | Accessor Method for the 'drop' slot in a 'genomicProfiles'... |
| drop-methods | ~~ Methods for Function 'drop' ~~ |
| evolve | Running the ChIPanalyser implementation of a Genetic... |
| generateStartingPopulation | Generate Starting population for ChIPanalyser Genetic... |
| 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"' |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| lambdaPWM | Accessor Method for the 'lambdaPWM' slot in a... |
| lambdaPWM_ | Setter Method for the 'lambdaPWM' slot in a... |
| lambdaPWM_--methods | ~~ Methods for Function 'lambdaPWM<-' ~~ |
| 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... |
| lociWidth_ | Setter Method for the 'lociWidth' slot in a... |
| lociWidth_--methods | ~~ Methods for Function 'lociWidth<-' ~~ |
| lociWidth-methods | ~~ Methods for Function 'lociWidth' ~~ |
| maxPWMScore | Accessor function for 'maxPWMScore' slot in a... |
| maxPWMScore-methods | ~~ Methods for Function 'maxPWMScore' ~~ |
| maxSignal | Accessor method for the 'maxSignal' slot in a... |
| maxSignal_- | Setter method for 'maxSignal' slot in a 'parameterOptions'... |
| maxSignal_--methods | ~~ Methods for Function 'maxSignal<-' ~~ |
| maxSignal-methods | ~~ Methods for Function 'maxSignal' ~~ |
| minPWMScore | Accessor method the 'minPWMScore' slot in a 'genomicProfiles'... |
| minPWMScore-methods | ~~ Methods for Function 'minPWMScore' ~~ |
| naturalLog | Accessor method the 'naturalLog' slot in a 'parameterOptions'... |
| naturalLog_- | Setter method for the 'naturalLog' slot in a... |
| naturalLog_--methods | ~~ Methods for Function 'naturalLog<-' ~~ |
| naturalLog-methods | ~~ Methods for Function 'naturalLog' ~~ |
| noiseFilter | Accessor Method for the 'noiseFilter' slot in a... |
| noiseFilter_ | Setter Method for the 'noiseFilter' slot in a... |
| noiseFilter_--methods | ~~ Methods for Function 'noiseFilter<-' ~~ |
| noiseFilter-methods | ~~ Methods for Function 'noiseFilter' ~~ |
| noOfSites | Accessor Method for the 'noOfSites' slot in a... |
| noOfSites_- | Setter Method for the 'noOfSites' slot in a... |
| noOfSites_--methods | ~~ Methods for Function 'noOfSites<-' ~~ |
| noOfSites-methods | ~~ Methods for Function 'noOfSites' ~~ |
| nos-class | Class '"nos"' |
| parameterOptions | parameter Options object |
| parameterOptions-class | Class '"parameterOptions"' |
| PFMFormat | Accesor method for the 'PFMFormat' slot in a... |
| PFMFormat_ | Setter method for the 'PFMFormat' slot in a 'genomicProfiles'... |
| PFMFormat_--methods | ~~ Methods for Function 'PFMFormat<-' ~~ |
| PFMFormat-methods | ~~ Methods for Function 'PFMFormat' ~~ |
| ploidy | Accessor method for the 'ploidy' slot in a 'parameterOptions'... |
| ploidy_- | Setter Method for the 'ploidy' slot in an 'parameterOptions'... |
| ploidy_--methods | ~~ Methods for Function 'ploidy<-' ~~ |
| 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'... |
| PositionFrequencyMatrix_- | Setter method for the 'PFM' slot in a 'genomicProfiles'... |
| PositionFrequencyMatrix_--methods | ~~ Methods for Function 'PositionFrequencyMatrix<-' ~~ |
| PositionFrequencyMatrix-methods | ~~ Methods for Function 'PositionFrequencyMatrix' ~~ |
| PositionWeightMatrix | Accessor Method for the 'PWM' slot in a 'genomicProfiles'... |
| PositionWeightMatrix_- | Setter Method for the 'PositionWeightMatrix' slot in a... |
| PositionWeightMatrix_--methods | ~~ Methods for Function 'PositionWeightMatrix<-' ~~ |
| PositionWeightMatrix-methods | ~~ Methods for Function 'PositionWeightMatrix' ~~ |
| processingChIP | Pre-processing ChIP-seq data |
| profileAccuracyEstimate | Estimating Accuracy of predicted Profiles |
| profiles-methods | ~~ Methods for Function 'profiles' ~~ |
| PWMpseudocount | Accessor Method for a 'PWMpseudocount' slot in a... |
| PWMpseudocount_- | Setter Method for the 'pseudocount' slot in a... |
| PWMpseudocount_--methods | ~~ Methods for Function 'PWMpseudocount<-' ~~ |
| PWMpseudocount-methods | ~~ Methods for Function 'PWMpseudocount' ~~ |
| PWMThreshold | Accessor method for the 'PWMThreshold' slot in a... |
| PWMThreshold_- | Setter Method for the 'PWMThreshold' slot in a... |
| PWMThreshold_--methods | ~~ Methods for Function 'PWMThreshold<-' ~~ |
| PWMThreshold-methods | ~~ Methods for Function 'PWMThreshold' ~~ |
| removeBackground | Accessor Method for the 'removeBackground' slot in a... |
| removeBackground_- | Setter Method for the 'removeBackground' slot in a... |
| removeBackground_--methods | ~~ Methods for Function 'removeBackground<-' ~~ |
| 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... |
| 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'... |
| stepSize_- | Setter Method for the 'stepSize' slot in a 'parameterOptions' |
| stepSize_--methods | ~~ Methods for Function 'stepSize<-' ~~ |
| stepSize-methods | ~~ Methods for Function 'stepSize' ~~ |
| strandRule | Accessor Method for the 'strandRule' slot in a... |
| strandRule_- | Setter method for the 'strandRule' slot in a... |
| strandRule_--methods | ~~ Methods for Function 'strandRule<-' ~~ |
| strandRule-methods | ~~ Methods for Function 'strandRule' ~~ |
| whichstrand | Accessor method for the 'whichstrand' slot in a... |
| whichstrand_- | Setter method for the 'whichstrand' slot in a... |
| whichstrand_--methods | ~~ Methods for Function 'whichstrand<-' ~~ |
| whichstrand-methods | ~~ Methods for Function 'whichstrand' ~~ |
