Global functions | |
---|---|
.AccessExtract | Source code |
.ChIPScore | Source code |
.DNASequenceLength<-,genomicProfilesInternal,vector-method | Man page |
.GoFCheck | Source code |
.GoFLoci | Source code |
.GoFPred | Source code |
.OptimalFormatConversion | Source code |
.ZeroBackground,parameterOptions-method | Man page |
.ZeroBackground<-,parameterOptions,vector-method | Man page |
.allMetrics | Source code |
.argsSwap | Source code |
.averageExpPWMScore<-,genomicProfilesInternal,numeric-method | Man page |
.cleanGoF | Source code |
.cleanUpAfterYourself | Source code |
.computeBPFrequency | Source code |
.computePWM | Source code |
.computePWMFromPFM | Source code |
.drop<-,genomicProfilesInternal,vector-method | Man page |
.extractionChIP | Source code |
.formatCheck | Source code |
.generateChIPProfile | Source code |
.generateChIPProfileRcpp | Source code |
.generatePWM,genomicProfilesInternal-method | Man page |
.genomicProfilesInternalContructor | Source code |
.geometricRatio | Source code |
.getIndexOfPWMThresholded | Source code |
.intMSE | Source code |
.internalChIPExtraction | Source code |
.internalChIPLoci | Source code |
.internalChIPLociSplit | Source code |
.internalChIPOccupValsLoci | Source code |
.internalChIPOccupValsParam | Source code |
.internalChIPParam | Source code |
.internalDNASequenceFromAccess | Source code |
.internalPWMScoreExt | Source code |
.internalUnlist | Source code |
.is.genomicProfiles | Source code |
.is.parameterOptions | Source code |
.maxPWMScore<-,genomicProfilesInternal,vector-method | Man page |
.meanGoFScore | Source code |
.methodSwitchGoF | Source code |
.minPWMScore<-,genomicProfilesInternal,vector-method | Man page |
.optimalExtraction | Source code |
.paramTag,parameterOptions-method | Man page |
.paramTag<-,parameterOptions,character-method | Man page |
.parameterShuffle | Source code |
.parseJASPARPFM | Source code |
.parsePFM | Source code |
.parsePFMFromFile | Source code |
.parseRawPFM | Source code |
.parseTransfacPFM | Source code |
.peakExtractionFScore | Source code |
.peakParametersExt | Source code |
.profiles<-,genomicProfilesInternal,GRList-method | Man page |
.scoreDNAStringSet | Source code |
.scoreReplace | Source code |
.sigmoidWeight | Source code |
.splitRanges | Source code |
.tags,genomicProfilesInternal-method | Man page |
.tags<-,genomicProfilesInternal,character-method | Man page |
.unpackMetrics | Source code |
.updateGenomicProfiles | Source code |
.vectorSmooth | Source code |
.what.is.ChIPScore | Source code |
.what.is.goodnessOfFit | Source code |
.what.is.occupancy | Source code |
.what.is.predictedProfile | Source code |
Access | Man page |
BPFrequency | Man page |
BPFrequency,genomicProfilesInternal-method | Man page |
BPFrequency-methods | Man page |
BPFrequency<- | Man page |
BPFrequency<-,genomicProfilesInternal,DNAStringSet-method | Man page |
BPFrequency<-,genomicProfilesInternal,vector-method | Man page |
BPFrequency<--methods | Man page |
ChIPScore-class | Man page |
ChIPanalyser | Man page |
ChIPanalyserData | Man page |
DNASequenceLength | Man page |
DNASequenceLength,genomicProfilesInternal-method | Man page |
DNASequenceLength-methods | Man page |
GRList-class | Man page |
PFMFormat | Man page |
PFMFormat,genomicProfilesInternal-method | Man page |
PFMFormat-methods | Man page |
PFMFormat<- | Man page |
PFMFormat<-,genomicProfilesInternal,character-method | Man page |
PFMFormat<--methods | Man page |
PWMThreshold | Man page |
PWMThreshold,parameterOptions-method | Man page |
PWMThreshold-methods | Man page |
PWMThreshold<- | Man page |
PWMThreshold<-,parameterOptions,numeric-method | Man page |
PWMThreshold<--methods | Man page |
PWMpseudocount | Man page |
PWMpseudocount,parameterOptions-method | Man page |
PWMpseudocount-methods | Man page |
PWMpseudocount<- | Man page |
PWMpseudocount<-,parameterOptions,numeric-method | Man page |
PWMpseudocount<--methods | Man page |
PositionFrequencyMatrix | Man page |
PositionFrequencyMatrix,genomicProfilesInternal-method | Man page |
PositionFrequencyMatrix-methods | Man page |
PositionFrequencyMatrix<- | Man page |
PositionFrequencyMatrix<-,genomicProfilesInternal,character-meth | Man page |
PositionFrequencyMatrix<-,genomicProfilesInternal,matrix-method | Man page |
PositionFrequencyMatrix<--methods | Man page |
PositionWeightMatrix | Man page |
PositionWeightMatrix,genomicProfilesInternal-method | Man page |
PositionWeightMatrix-methods | Man page |
PositionWeightMatrix<- | Man page |
PositionWeightMatrix<-,genomicProfilesInternal,matrix-method | Man page |
PositionWeightMatrix<--methods | Man page |
averageExpPWMScore | Man page |
averageExpPWMScore,genomicProfilesInternal-method | Man page |
averageExpPWMScore-methods | Man page |
backgroundSignal | Man page |
backgroundSignal,parameterOptions-method | Man page |
backgroundSignal-methods | Man page |
backgroundSignal<- | Man page |
backgroundSignal<-,parameterOptions,numeric-method | Man page |
backgroundSignal<--methods | Man page |
boundMolecules | Man page |
boundMolecules,parameterOptions-method | Man page |
boundMolecules-methods | Man page |
boundMolecules<- | Man page |
boundMolecules<-,parameterOptions,vector-method | Man page |
boundMolecules<--methods | Man page |
chipMean | Man page |
chipMean,parameterOptions-method | Man page |
chipMean-methods | Man page |
chipMean<- | Man page |
chipMean<-,parameterOptions,numeric-method | Man page |
chipMean<--methods | Man page |
chipSd | Man page |
chipSd,parameterOptions-method | Man page |
chipSd-methods | Man page |
chipSd<- | Man page |
chipSd<-,parameterOptions,numeric-method | Man page |
chipSd<--methods | Man page |
chipSmooth | Man page |
chipSmooth,parameterOptions-method | Man page |
chipSmooth-methods | Man page |
chipSmooth<- | Man page |
chipSmooth<-,parameterOptions,vector-method | Man page |
chipSmooth<--methods | Man page |
computeChIPProfile | Man page Source code |
computeGenomeWideScores | Man page Source code |
computeOccupancy | Man page Source code |
computeOptimal | Man page Source code |
computePWMScore | Man page Source code |
drop | Man page |
drop,genomicProfilesInternal-method | Man page |
drop-methods | Man page |
eveLocus | Man page |
eveLocusChip | Man page |
geneRef | Man page |
genomicProfiles | Man page Source code |
genomicProfiles-class | Man page |
genomicProfilesInternal-class | Man page |
initialize,ChIPScore-method | Man page |
initialize,genomicProfiles-method | Man page |
initialize,parameterOptions-method | Man page |
initialize-methods | Man page |
lambdaPWM | Man page |
lambdaPWM,parameterOptions-method | Man page |
lambdaPWM-methods | Man page |
lambdaPWM<- | Man page |
lambdaPWM<-,parameterOptions,vector-method | Man page |
lambdaPWM<--methods | Man page |
loci | Man page |
loci,ChIPScore-method | Man page |
loci-class | Man page |
loci-methods | Man page |
lociWidth | Man page |
lociWidth,parameterOptions-method | Man page |
lociWidth-methods | Man page |
lociWidth<- | Man page |
lociWidth<-,parameterOptions,numeric-method | Man page |
lociWidth<--methods | Man page |
maxPWMScore | Man page |
maxPWMScore,genomicProfilesInternal-method | Man page |
maxPWMScore-methods | Man page |
maxSignal | Man page |
maxSignal,parameterOptions-method | Man page |
maxSignal-methods | Man page |
maxSignal<- | Man page |
maxSignal<-,parameterOptions,numeric-method | Man page |
maxSignal<--methods | Man page |
minPWMScore | Man page |
minPWMScore,genomicProfilesInternal-method | Man page |
minPWMScore-methods | Man page |
naturalLog | Man page |
naturalLog,parameterOptions-method | Man page |
naturalLog-methods | Man page |
naturalLog<- | Man page |
naturalLog<-,parameterOptions,logical-method | Man page |
naturalLog<--methods | Man page |
noOfSites | Man page |
noOfSites,parameterOptions-method | Man page |
noOfSites-methods | Man page |
noOfSites<- | Man page |
noOfSites<-,parameterOptions,character-method | Man page |
noOfSites<-,parameterOptions,numeric-method | Man page |
noOfSites<--methods | Man page |
noiseFilter | Man page |
noiseFilter,parameterOptions-method | Man page |
noiseFilter-methods | Man page |
noiseFilter<- | Man page |
noiseFilter<-,parameterOptions,character-method | Man page |
noiseFilter<--methods | Man page |
nos-class | Man page |
parameterOptions | Man page Source code |
parameterOptions-class | Man page |
ploidy | Man page |
ploidy,parameterOptions-method | Man page |
ploidy-methods | Man page |
ploidy<- | Man page |
ploidy<-,parameterOptions,numeric-method | Man page |
ploidy<--methods | Man page |
plotOccupancyProfile | Man page Source code |
plotOptimalHeatMaps | Man page Source code |
processingChIP | Man page Source code |
profileAccuracyEstimate | Man page Source code |
profiles | Man page |
profiles,genomicProfilesInternal-method | Man page |
removeBackground | Man page |
removeBackground,parameterOptions-method | Man page |
removeBackground-methods | Man page |
removeBackground<- | Man page |
removeBackground<-,parameterOptions,vector-method | Man page |
removeBackground<--methods | Man page |
scores | Man page |
scores,ChIPScore-method | Man page |
scores-methods | Man page |
searchSites | Man page Source code |
show,ChIPScore-method | Man page |
show,genomicProfiles-method | Man page |
show,parameterOptions-method | Man page |
show-methods | Man page |
stepSize | Man page |
stepSize,parameterOptions-method | Man page |
stepSize-methods | Man page |
stepSize<- | Man page |
stepSize<-,parameterOptions,numeric-method | Man page |
stepSize<--methods | Man page |
strandRule | Man page |
strandRule,parameterOptions-method | Man page |
strandRule-methods | Man page |
strandRule<- | Man page |
strandRule<-,parameterOptions,character-method | Man page |
strandRule<--methods | Man page |
whichstrand | Man page |
whichstrand,parameterOptions-method | Man page |
whichstrand-methods | Man page |
whichstrand<- | Man page |
whichstrand<-,parameterOptions,character-method | Man page |
whichstrand<--methods | Man page |
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