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"' |