Man pages for ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding Sites

AllSitesAboveThresholdAccessor for 'AllSitesAboveThreshold' slot in a...
averageExpPWMScoreAccessor for 'averageExpPWMScore' slot in a...
backgroundSignalAccessor method for the 'backgroundSignal' slot in a...
backgroundSignal_-Setter method for 'backgroundSignal' slot in a...
boundMoleculesAccessor methods for 'boundMolecules' slot in...
boundMolecules_-Setter method for the 'boundMolecules' slot in a...
BPFrequencyAccessor method for 'BPFrequency' slot in a...
BPFrequency_-Setter method for 'BPFrequency' slot in a...
ChIPanalyser-packageChIPanalyser: Predicting Transcription Factor Binding Sites
chipMeanAccessor method for 'chipMean' slot in a...
chipMean_-Access methods for 'chipMean' slot in...
chipSdAccessor method for 'chipSd' slot in a...
chipSd_-Setter methods for 'chipSd' slot in a...
chipSmoothAccessor methods for 'chipSmooth' slot in a...
chipSmooth_-Setter method for 'chipSmooth' slot in...
computeChipProfileComputing ChIP-seq like profiles from Occupancy data.
computeGenomeWidePWMScoreComputing genome wide PWM scores.
computeOccupancyCompute Occupancy values from PWM Scores based on model.
computeOptimalcompute Optimal Parameters
computePWMScoreCompute PWM Scores of sites above threshold.
dataChIPanalyserData
DNASequenceLengthAccessor method for 'DNASequenceLength' slot in a...
DNASequenceLength_-Setter Method for 'DNASequenceLength' slot in a...
genomicProfileParametersGenomic Profile Parameter Object
genomicProfileParameters-classClass '"genomicProfileParameters"'
GRList-classClass '"GRList"'
maxPWMScoreAccessor function for 'maxPWMScore' slot in a...
maxSignalAccessor method for the 'maxSignal' slot in a...
maxSignal_-Setter method for 'maxSignal' slot in a...
minPWMScoreAccessor method the 'minPWMScore' slot in a...
naturalLogAccessor method the 'naturalLog' slot in a...
naturalLog_-Setter method for the 'naturalLog' slot in a...
NoAccessAccessor Method for the 'NoAccess' slot in a...
noOfSitesAccessor Method for the 'noOfSites' slot in a...
noOfSites_-Setter Method for the 'noOfSites' slot in a...
occupancyProfileParametersOccupancy Profile Parameters
occupancyProfileParameters-classClass '"occupancyProfileParameters"'
PFMFormatAccesor method for the 'PFMFormat' slot in a...
PFMFormat_Setter method for the 'PFMFormat' slot in a...
ploidyAccessor method for the 'ploidy' slot in a...
ploidy_-Setter Method for the 'ploidy' slot in an...
plotOccupancyProfilePlot Occupancy Profiles
plotOptimalHeatMapsHeat Map of optimal Parameters
PositionFrequencyMatrixAccessor method for the 'PFM' slot in a...
PositionFrequencyMatrix_-Setter method for the 'PFM' slot in a...
PositionWeightMatrixAccessor Method for the 'PWM' slot in a...
PositionWeightMatrix_-Setter Method for the 'PositionWeightMatrix' slot in a...
processingChIPseqPre-processing ChIP-seq data from UCSC format file
profileAccuracyEstimateEstimating Accuracy of predicted Profiles
PWMpseudocountAccessor Method for a 'PWMpseudocount' slot in a...
PWMpseudocount_-Setter Method for the 'pseudocount' slot in a...
PWMThresholdAccessor method for the 'PWMThreshold' slot in a...
PWMThreshold_-Setter Method for the 'PWMThreshold' slot in a...
removeBackgroundAccessor Method for the 'removeBackground' slot in a...
removeBackground_-Setter Method for the 'removeBackground' slot in a...
ScalingFactorPWMAccessor method for the 'lambda' slot in a...
ScalingFactorPWM_-Setter method for the 'lambda' slot in a...
searchSitesSearching function for Sites above threshold and predicted...
stepSizeAccessor method of the 'stepSize' slot in...
stepSize_-Setter Method for the 'stepSize' slot in a...
strandRuleAccessor Method for the 'strandRule' slot in a...
strandRule_-Setter method for the 'strandRule' slot in a...
whichstrandAccessor method for the 'whichstrand' slot in a...
whichstrand_-Setter method for the 'whichstrand' slot in a...
ChIPanalyser documentation built on Nov. 1, 2018, 2:18 a.m.