# CHiCAGO: Capture Hi-C Analysis of Genomic Organization

## Documentation for package ‘Chicago’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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