Chicago-package	Chicago-package
cdUnitTest	cdUnitTest
Chicago	Chicago-package
chicagoData	chicagoData
chicagoPipeline	chicagoPipeline
copyCD	copyCD
defaultSettings	defaultSettings
estimateBrownianComponent	estimateBrownianComponent
estimateBrownianNoise	estimateBrownianComponent
estimateDistFun	estimateDistFun
estimateTechnicalNoise	estimateTechnicalNoise
exportResults	exportResults
exportToGI	exportResults
getPvals	getPvals
getScores	getScores
getSkOnly	getSkOnly
intData	chicagoData
intData,chicagoData-method	chicagoData
intData<-	chicagoData
intData<-,chicagoData-method	chicagoData
mergeSamples	mergeSamples
modifySettings	modifySettings
normaliseBaits	normaliseBaits
normaliseOtherEnds	normaliseOtherEnds
overlapFragWithFeatures	overlapFragWithFeatures
params	chicagoData
params,chicagoData-method	chicagoData
params<-	chicagoData
params<-,chicagoData-method	chicagoData
peakEnrichment4Features	peakEnrichment4Features
plotBaits	plotBaits
plotDistFun	plotDistFun
readAndMerge	readAndMerge
readSample	readSample
setExperiment	setExperiment
settings	chicagoData
settings,chicagoData-method	chicagoData
