# ChIPanalyser: Predicting Transcription Factor Binding Sites

## Documentation for package ‘ChIPanalyser’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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-method | Class '"occupancyProfileParameters"'
thetaThreshold<--method | Class '"occupancyProfileParameters"'

## -- 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"'