# ChIPanalyser: Predicting Transcription Factor Binding Sites

## Documentation for package ‘ChIPanalyser’ version 1.31.0

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

## Help Pages

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

## -- A --

Access | ChIPanalyserData
averageExpPWMScore | Accessor for 'averageExpPWMScore' slot in a 'genomicProfiles' object.
averageExpPWMScore-method | Class '"genomicProfilesInternal"'
averageExpPWMScore-methods | ~~ Methods for Function 'averageExpPWMScore' ~~

## -- B --

backgroundSignal | Accessor method for the 'backgroundSignal' slot in a 'parameterOptions' object.
backgroundSignal-method | Class '"parameterOptions"'
backgroundSignal-methods | ~~ Methods for Function 'backgroundSignal' ~~
backgroundSignal<- | Setter method for 'backgroundSignal' slot in a 'parameterOptions'
backgroundSignal<--method | Class '"parameterOptions"'
backgroundSignal<--methods | ~~ Methods for Function 'backgroundSignal<-' ~~
boundMolecules | Accessor methods for 'boundMolecules' slot in 'parameterOptions' object.
boundMolecules-method | Class '"parameterOptions"'
boundMolecules-methods | ~~ Methods for Function 'boundMolecules' ~~
boundMolecules<- | Setter method for the 'boundMolecules' slot in a 'parameterOptions' object.
boundMolecules<--method | Class '"parameterOptions"'
boundMolecules<--methods | ~~ Methods for Function 'boundMolecules<-' ~~
BPFrequency | Accessor method for 'BPFrequency' slot in a 'genomicProfiles' object.
BPFrequency-method | Class '"genomicProfilesInternal"'
BPFrequency-methods | ~~ Methods for Function 'BPFrequency' ~~
BPFrequency<- | Setter method for 'BPFrequency' slot in a 'genomicProfiles' object.
BPFrequency<--method | Class '"genomicProfilesInternal"'
BPFrequency<--methods | ~~ Methods for Function 'BPFrequency<-' ~~

## -- C --

chip | ChIPanalyserData
ChIPanalyser | ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyserData | ChIPanalyserData
chipMean | Accessor method for 'chipMean' slot in a 'parameterOptions' object.
chipMean-method | Class '"parameterOptions"'
chipMean-methods | ~~ Methods for Function 'chipMean' ~~
chipMean<- | Access methods for 'chipMean' slot in 'parameterOptions' object.
chipMean<--method | Class '"parameterOptions"'
chipMean<--methods | ~~ Methods for Function 'chipMean<-' ~~
ChIPScore-class | Class '"ChIPScore"'
chipSd | Accessor method for 'chipSd' slot in a 'parameterOptions' object.
chipSd-method | Class '"parameterOptions"'
chipSd-methods | ~~ Methods for Function 'chipSd' ~~
chipSd<- | Setter methods for 'chipSd' slot in a 'parameterOptions' object.
chipSd<--method | Class '"parameterOptions"'
chipSd<--methods | ~~ Methods for Function 'chipSd<-' ~~
chipSmooth | Accessor methods for 'chipSmooth' slot in a 'parameterOptions' object.
chipSmooth-method | Class '"parameterOptions"'
chipSmooth-methods | ~~ Methods for Function 'chipSmooth' ~~
chipSmooth<- | Setter method for 'chipSmooth' slot in 'parameterOptions' object.
chipSmooth<--method | Class '"parameterOptions"'
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.
cs | ChIPanalyserData

## -- D --

DNASequenceLength | Accessor method for 'DNASequenceLength' slot in a 'genomicProfiles'
DNASequenceLength-method | Class '"genomicProfilesInternal"'
DNASequenceLength-methods | ~~ Methods for Function 'DNASequenceLength' ~~
drop | Accessor Method for the 'drop' slot in a 'genomicProfiles' object.
drop-method | Class '"genomicProfilesInternal"'
drop-methods | ~~ Methods for Function 'drop' ~~

## -- E --

evolve | Running the ChIPanalyser implementation of a Genetic algorithm.

## -- G --

generateStartingPopulation | Generate Starting population for ChIPanalyser Genetic algortihm
geneRef | ChIPanalyserData
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"'

## -- I --

initialize-method | ~~ Methods for Function 'initialize' ~~
initialize-methods | ~~ Methods for Function 'initialize' ~~

## -- L --

lambdaPWM | Accessor Method for the 'lambdaPWM' slot in a 'parameterOptions' object
lambdaPWM-method | Class '"parameterOptions"'
lambdaPWM-methods | ~~ Methods for Function 'lambdaPWM' ~~
lambdaPWM<- | Setter Method for the 'lambdaPWM' slot in a 'parameterOptions' object
lambdaPWM<--method | Class '"parameterOptions"'
lambdaPWM<--methods | ~~ Methods for Function 'lambdaPWM<-' ~~
loci | Accessor Method for the 'loci' slot in a 'ChIPScore' object
loci-class | Class '"loci"'
loci-method | Class '"ChIPScore"'
loci-methods | ~~ Methods for Function 'loci' ~~
lociWidth | Accessor Method for the 'lociWidth' slot in a 'parameterOptions' object
lociWidth-method | Class '"parameterOptions"'
lociWidth-methods | ~~ Methods for Function 'lociWidth' ~~
lociWidth<- | Setter Method for the 'lociWidth' slot in a 'parameterOptions' object
lociWidth<--method | Class '"parameterOptions"'
lociWidth<--methods | ~~ Methods for Function 'lociWidth<-' ~~

## -- M --

maxPWMScore | Accessor function for 'maxPWMScore' slot in a 'genomicProfiles' object.
maxPWMScore-method | Class '"genomicProfilesInternal"'
maxPWMScore-methods | ~~ Methods for Function 'maxPWMScore' ~~
maxSignal | Accessor method for the 'maxSignal' slot in a 'parameterOptions' object.
maxSignal-method | Class '"parameterOptions"'
maxSignal-methods | ~~ Methods for Function 'maxSignal' ~~
maxSignal<- | Setter method for 'maxSignal' slot in a 'parameterOptions' object.
maxSignal<--method | Class '"parameterOptions"'
maxSignal<--methods | ~~ Methods for Function 'maxSignal<-' ~~
minPWMScore | Accessor method the 'minPWMScore' slot in a 'genomicProfiles' object
minPWMScore-method | Class '"genomicProfilesInternal"'
minPWMScore-methods | ~~ Methods for Function 'minPWMScore' ~~

## -- N --

naturalLog | Accessor method the 'naturalLog' slot in a 'parameterOptions' object.
naturalLog-method | Class '"parameterOptions"'
naturalLog-methods | ~~ Methods for Function 'naturalLog' ~~
naturalLog<- | Setter method for the 'naturalLog' slot in a 'parameterOptions' object.
naturalLog<--method | Class '"parameterOptions"'
naturalLog<--methods | ~~ Methods for Function 'naturalLog<-' ~~
noiseFilter | Accessor Method for the 'noiseFilter' slot in a 'parameterOptions' object
noiseFilter-method | Class '"parameterOptions"'
noiseFilter-methods | ~~ Methods for Function 'noiseFilter' ~~
noiseFilter<- | Setter Method for the 'noiseFilter' slot in a 'parameterOptions' object
noiseFilter<--method | Class '"parameterOptions"'
noiseFilter<--methods | ~~ Methods for Function 'noiseFilter<-' ~~
noOfSites | Accessor Method for the 'noOfSites' slot in a 'parameterOptions' object
noOfSites-method | Class '"parameterOptions"'
noOfSites-methods | ~~ Methods for Function 'noOfSites' ~~
noOfSites<- | Setter Method for the 'noOfSites' slot in a 'parameterOptions' object.
noOfSites<--method | Class '"parameterOptions"'
noOfSites<--methods | ~~ Methods for Function 'noOfSites<-' ~~
nos-class | Class '"nos"'

## -- P --

parameterOptions | parameter Options object
parameterOptions-class | Class '"parameterOptions"'
PFMFormat | Accesor method for the 'PFMFormat' slot in a 'genomicProfiles' object
PFMFormat-method | Class '"genomicProfilesInternal"'
PFMFormat-methods | ~~ Methods for Function 'PFMFormat' ~~
PFMFormat<- | Setter method for the 'PFMFormat' slot in a 'genomicProfiles' object
PFMFormat<--method | Class '"genomicProfilesInternal"'
PFMFormat<--methods | ~~ Methods for Function 'PFMFormat<-' ~~
ploidy | Accessor method for the 'ploidy' slot in a 'parameterOptions' object
ploidy-method | Class '"parameterOptions"'
ploidy-methods | ~~ Methods for Function 'ploidy' ~~
ploidy<- | Setter Method for the 'ploidy' slot in an 'parameterOptions' object
ploidy<--method | Class '"parameterOptions"'
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' object
PositionFrequencyMatrix-method | Class '"genomicProfilesInternal"'
PositionFrequencyMatrix-methods | ~~ Methods for Function 'PositionFrequencyMatrix' ~~
PositionFrequencyMatrix<- | Setter method for the 'PFM' slot in a 'genomicProfiles' object
PositionFrequencyMatrix<--method | Class '"genomicProfilesInternal"'
PositionFrequencyMatrix<--methods | ~~ Methods for Function 'PositionFrequencyMatrix<-' ~~
PositionWeightMatrix | Accessor Method for the 'PWM' slot in a 'genomicProfiles' object
PositionWeightMatrix-method | Class '"genomicProfilesInternal"'
PositionWeightMatrix-methods | ~~ Methods for Function 'PositionWeightMatrix' ~~
PositionWeightMatrix<- | Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfiles' object
PositionWeightMatrix<--method | Class '"genomicProfilesInternal"'
PositionWeightMatrix<--methods | ~~ Methods for Function 'PositionWeightMatrix<-' ~~
processingChIP | Pre-processing ChIP-seq data
profileAccuracyEstimate | Estimating Accuracy of predicted Profiles
profiles | ~~ Methods for Function 'profiles' ~~
profiles-method | Class '"genomicProfilesInternal"'
PWMpseudocount | Accessor Method for a 'PWMpseudocount' slot in a 'parameterOptions'
PWMpseudocount-method | Class '"parameterOptions"'
PWMpseudocount-methods | ~~ Methods for Function 'PWMpseudocount' ~~
PWMpseudocount<- | Setter Method for the 'pseudocount' slot in a 'parameterOptions' object
PWMpseudocount<--method | Class '"parameterOptions"'
PWMpseudocount<--methods | ~~ Methods for Function 'PWMpseudocount<-' ~~
PWMThreshold | Accessor method for the 'PWMThreshold' slot in a 'parameterOptions' object
PWMThreshold-method | Class '"parameterOptions"'
PWMThreshold-methods | ~~ Methods for Function 'PWMThreshold' ~~
PWMThreshold<- | Setter Method for the 'PWMThreshold' slot in a 'parameterOptions' object
PWMThreshold<--method | Class '"parameterOptions"'
PWMThreshold<--methods | ~~ Methods for Function 'PWMThreshold<-' ~~

## -- R --

removeBackground | Accessor Method for the 'removeBackground' slot in a 'parameterOptions' object
removeBackground-method | Class '"parameterOptions"'
removeBackground-methods | ~~ Methods for Function 'removeBackground' ~~
removeBackground<- | Setter Method for the 'removeBackground' slot in a 'parameterOptions' object
removeBackground<--method | Class '"parameterOptions"'
removeBackground<--methods | ~~ Methods for Function 'removeBackground<-' ~~

## -- S --

scores | Accessor Method for the 'scores' slot in a 'ChIPScore' object
scores-method | Class '"ChIPScore"'
scores-methods | ~~ Methods for Function 'scores' ~~
searchSites | Searching function for Sites above threshold and predicted ChIP-seq Profiles
setChromatinStates | setChromatinStates
show-method | ~~ Methods for Function 'show' ~~
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' object
stepSize-method | Class '"parameterOptions"'
stepSize-methods | ~~ Methods for Function 'stepSize' ~~
stepSize<- | Setter Method for the 'stepSize' slot in a 'parameterOptions'
stepSize<--method | Class '"parameterOptions"'
stepSize<--methods | ~~ Methods for Function 'stepSize<-' ~~
strandRule | Accessor Method for the 'strandRule' slot in a 'parameterOptions' object
strandRule-method | Class '"parameterOptions"'
strandRule-methods | ~~ Methods for Function 'strandRule' ~~
strandRule<- | Setter method for the 'strandRule' slot in a 'parameterOptions' object.
strandRule<--method | Class '"parameterOptions"'
strandRule<--methods | ~~ Methods for Function 'strandRule<-' ~~

## -- T --

top | ChIPanalyserData

## -- W --

whichstrand | Accessor method for the 'whichstrand' slot in a 'parameterOptions' object
whichstrand-method | Class '"parameterOptions"'
whichstrand-methods | ~~ Methods for Function 'whichstrand' ~~
whichstrand<- | Setter method for the 'whichstrand' slot in a 'parameterOptions' object
whichstrand<--method | Class '"parameterOptions"'
whichstrand<--methods | ~~ Methods for Function 'whichstrand<-' ~~

## -- misc --

.averageExpPWMScore<--method | Class '"genomicProfilesInternal"'
.DNASequenceLength<--method | Class '"genomicProfilesInternal"'
.drop<--method | Class '"genomicProfilesInternal"'
.generatePWM-method | Class '"genomicProfilesInternal"'
.maxPWMScore<--method | Class '"genomicProfilesInternal"'
.minPWMScore<--method | Class '"genomicProfilesInternal"'
.paramTag-method | Class '"parameterOptions"'
.paramTag<--method | Class '"parameterOptions"'
.profiles<--method | Class '"genomicProfilesInternal"'
.tags-method | Class '"genomicProfilesInternal"'
.tags<--method | Class '"genomicProfilesInternal"'
.ZeroBackground-method | Class '"parameterOptions"'
.ZeroBackground<--method | Class '"parameterOptions"'