API for patrickCNMartin/ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding Sites

Global functions
.ZeroBackground,genomicProfileParameters-method Man page
.ZeroBackground<-,genomicProfileParameters,vector-method Man page
Access Man page
AllSitesAboveThreshold Man page
AllSitesAboveThreshold,genomicProfileParameters-method Man page
AllSitesAboveThreshold-methods Man page
AllSitesAboveThresholdReplace Source code
BPFrequency Man page
BPFrequency,genomicProfileParameters-method Man page
BPFrequency-methods Man page
BPFrequency<- Man page
BPFrequency<-,genomicProfileParameters,DNAStringSet-method Man page
BPFrequency<-,genomicProfileParameters,vector-method Man page
BPFrequency<--methods Man page
ChIPanalyser Man page
ChIPanalyserData Man page
DNASequenceLength Man page
DNASequenceLength,genomicProfileParameters-method Man page
DNASequenceLength-methods Man page
DNASequenceLength<- Man page
DNASequenceLength<-,genomicProfileParameters,vector-method Man page
DNASequenceLength<--methods Man page
GRList-class Man page
NoAccess Man page
NoAccess,genomicProfileParameters-method Man page
NoAccess-methods Man page
NoAccessReplace Source code
PFMFormat Man page
PFMFormat,genomicProfileParameters-method Man page
PFMFormat-methods Man page
PFMFormat<- Man page
PFMFormat<-,genomicProfileParameters,character-method Man page
PFMFormat<--methods Man page
PWMThreshold Man page
PWMThreshold,genomicProfileParameters-method Man page
PWMThreshold-methods Man page
PWMThreshold<- Man page
PWMThreshold<-,genomicProfileParameters,numeric-method Man page
PWMThreshold<--methods Man page
PWMpseudocount Man page
PWMpseudocount,genomicProfileParameters-method Man page
PWMpseudocount-methods Man page
PWMpseudocount<- Man page
PWMpseudocount<-,genomicProfileParameters,numeric-method Man page
PWMpseudocount<--methods Man page
PositionFrequencyMatrix Man page
PositionFrequencyMatrix,genomicProfileParameters-method Man page
PositionFrequencyMatrix-methods Man page
PositionFrequencyMatrix<- Man page
PositionFrequencyMatrix<-,genomicProfileParameters,character-met Man page
PositionFrequencyMatrix<-,genomicProfileParameters,matrix-method Man page
PositionFrequencyMatrix<--methods Man page
PositionWeightMatrix Man page
PositionWeightMatrix,genomicProfileParameters-method Man page
PositionWeightMatrix-methods Man page
PositionWeightMatrix<- Man page
PositionWeightMatrix<-,genomicProfileParameters,matrix-method Man page
PositionWeightMatrix<--methods Man page
ScalingFactorPWM Man page
ScalingFactorPWM,genomicProfileParameters-method Man page
ScalingFactorPWM-methods Man page
ScalingFactorPWM<- Man page
ScalingFactorPWM<-,genomicProfileParameters,vector-method Man page
ScalingFactorPWM<--methods Man page
ZeroBackground Source code
ZeroBackgroundReplace Source code
averageExpPWMScore Man page
averageExpPWMScore,genomicProfileParameters-method Man page
averageExpPWMScore-methods Man page
averageExpPWMScoreReplace Source code
backgroundSignal Man page
backgroundSignal,occupancyProfileParameters-method Man page
backgroundSignal-methods Man page
backgroundSignal<- Man page
backgroundSignal<-,occupancyProfileParameters,numeric-method Man page
backgroundSignal<--methods Man page
boundMolecules Man page
boundMolecules,occupancyProfileParameters-method Man page
boundMolecules-methods Man page
boundMolecules<- Man page
boundMolecules<-,occupancyProfileParameters,vector-method Man page
boundMolecules<--methods Man page
chipMean Man page
chipMean,occupancyProfileParameters-method Man page
chipMean-methods Man page
chipMean<- Man page
chipMean<-,occupancyProfileParameters,numeric-method Man page
chipMean<--methods Man page
chipSd Man page
chipSd,occupancyProfileParameters-method Man page
chipSd-methods Man page
chipSd<- Man page
chipSd<-,occupancyProfileParameters,numeric-method Man page
chipSd<--methods Man page
chipSmooth Man page
chipSmooth,occupancyProfileParameters-method Man page
chipSmooth-methods Man page
chipSmooth<- Man page
chipSmooth<-,occupancyProfileParameters,vector-method Man page
chipSmooth<--methods Man page
computeBPFrequency Source code
computeChipProfile Man page Source code
computeGenomeWidePWMScore Man page Source code
computeOccupancy Man page Source code
computeOptimal Man page Source code
computePWM Source code
computePWMFromPFM Source code
computePWMScore Man page Source code
computeTheta Source code
eveLocus Man page
eveLocusChip Man page
geneRef Man page
generateChIPProfile Source code
generateChIPProfileRcpp Source code
genomicProfileParameters Man page Source code
genomicProfileParameters-class Man page
getIndexOfPWMThresholded Source code
maxPWMScore Man page
maxPWMScore,genomicProfileParameters-method Man page
maxPWMScore-methods Man page
maxPWMScoreReplace Source code
maxSignal Man page
maxSignal,occupancyProfileParameters-method Man page
maxSignal-methods Man page
maxSignal<- Man page
maxSignal<-,occupancyProfileParameters,numeric-method Man page
maxSignal<--methods Man page
minPWMScore Man page
minPWMScore,genomicProfileParameters-method Man page
minPWMScore-methods Man page
minPWMScoreReplace Source code
naturalLog Man page
naturalLog,genomicProfileParameters-method Man page
naturalLog-methods Man page
naturalLog<- Man page
naturalLog<-,genomicProfileParameters,logical-method Man page
naturalLog<--methods Man page
noOfSites Man page
noOfSites,genomicProfileParameters-method Man page
noOfSites-methods Man page
noOfSites<- Man page
noOfSites<-,genomicProfileParameters,vector-method Man page
noOfSites<--methods Man page
occupancyProfileParameters Man page Source code
occupancyProfileParameters-class Man page
parseJASPARPFM Source code
parsePFM Source code
parsePFMFromFile Source code
parseRawPFM Source code
parseTransfacPFM Source code
ploidy Man page
ploidy,occupancyProfileParameters-method Man page
ploidy-methods Man page
ploidy<- Man page
ploidy<-,occupancyProfileParameters,numeric-method Man page
ploidy<--methods Man page
plotOccupancyProfile Man page Source code
plotOptimalHeatMaps Man page Source code
profileAccuracyEstimate Man page Source code
removeBackground Man page
removeBackground,occupancyProfileParameters-method Man page
removeBackground-methods Man page
removeBackground<- Man page
removeBackground<-,occupancyProfileParameters,vector-method Man page
removeBackground<--methods Man page
s.PWMScoreComputed Source code
s.genomeWideComputed Source code
s.genomicProfileParameter Source code
s.occupancyProfileParameters Source code
scoreDNAStringSet Source code
searchSites Man page Source code
show,occupancyProfileParameters-method Man page
stepSize Man page
stepSize,occupancyProfileParameters-method Man page
stepSize-methods Man page
stepSize<- Man page
stepSize<-,occupancyProfileParameters,numeric-method Man page
stepSize<--methods Man page
strandRule Man page
strandRule,genomicProfileParameters-method Man page
strandRule-methods Man page
strandRule<- Man page
strandRule<-,genomicProfileParameters,character-method Man page
strandRule<--methods Man page
thetaThreshold Man page
thetaThreshold,occupancyProfileParameters-method Man page
thetaThreshold-methods Man page
thetaThreshold<- Man page
thetaThreshold<-,occupancyProfileParameters,numeric-method Man page
thetaThreshold<--methods Man page
whichstrand Man page
whichstrand,genomicProfileParameters-method Man page
whichstrand-methods Man page
whichstrand<- Man page
whichstrand<-,genomicProfileParameters,character-method Man page
whichstrand<--methods Man page
patrickCNMartin/ChIPanalyser documentation built on Oct. 18, 2017, 10:21 p.m.