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' ~~ |
genomicProfiles | Genomic Profile object |
genomicProfiles-class | Class '"genomicProfiles"' |
genomicProfilesInternal-class | Class '"genomicProfilesInternal"' |
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... |
show-methods | ~~ Methods for Function 'show' ~~ |
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' ~~ |
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