Chicago-package         CHiCAGO: Capture Hi-C Analysis of Genomic
                        Organization
cdUnitTest              ChicagoData object for unit testing
chicagoData             The 'chicagoData' class.
chicagoPipeline         CHiCAGO pipeline function
copyCD                  Copy chicagoData object
defaultSettings         Default CHiCAGO settings
estimateBrownianComponent
                        Estimate Brownian background component.
estimateDistFun         Estimate the Distance Function
estimateTechnicalNoise
                        Estimate Technical Noise
exportResults           Export Results
getPvals                Get P-values
getScores               Get CHiCAGO scores.
getSkOnly               Get S_k factors from multiple replicates
mergeSamples            Merge samples together.
modifySettings          Modify Settings
normaliseBaits          Normalise Baits
normaliseOtherEnds      Normalise Other Ends
overlapFragWithFeatures
                        Overlap Other-Ends with Features
peakEnrichment4Features
                        Enrichment for Features
plotBaits               Plot Baits
plotDistFun             Plot the Distance Function
readAndMerge            Read And Merge
readSample              Read Sample
setExperiment           Set Experiment
