ChIPanalyser: Predicting Transcription Factor Binding Sites


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Documentation for package ‘ChIPanalyser’ version 1.2.0

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A B C D E G M N O P R S T W misc

-- A --

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.

-- B --

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.

-- C --

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.

-- D --

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.

-- E --

eveLocus ChIPanalyserData
eveLocusChip ChIPanalyserData

-- G --

geneRef ChIPanalyserData
genomicProfileParameters Genomic Profile Parameter Object
genomicProfileParameters-class Class '"genomicProfileParameters"'
GRList-class Class '"GRList"'

-- M --

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

-- N --

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.

-- O --

occupancyProfileParameters Occupancy Profile Parameters
occupancyProfileParameters-class Class '"occupancyProfileParameters"'

-- P --

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

-- R --

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

-- S --

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.

-- T --

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

-- W --

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

-- misc --

.ZeroBackground-method Class '"genomicProfileParameters"'
.ZeroBackground<--method Class '"genomicProfileParameters"'