Man pages for Chicago
CHiCAGO: Capture Hi-C Analysis of Genomic Organization

cdUnitTestChicagoData object for unit testing
chicagoDataThe 'chicagoData' class.
Chicago-packageCHiCAGO: Capture Hi-C Analysis of Genomic Organization
chicagoPipelineCHiCAGO pipeline function
copyCDCopy chicagoData object
defaultSettingsDefault CHiCAGO settings
estimateBrownianComponentEstimate Brownian background component.
estimateDistFunEstimate the Distance Function
estimateTechnicalNoiseEstimate Technical Noise
exportResultsExport Results
getPvalsGet P-values
getScoresGet CHiCAGO scores.
getSkOnlyGet S_k factors from multiple replicates
mergeSamplesMerge samples together.
modifySettingsModify Settings
normaliseBaitsNormalise Baits
normaliseOtherEndsNormalise Other Ends
overlapFragWithFeaturesOverlap Other-Ends with Features
peakEnrichment4FeaturesEnrichment for Features
plotBaitsPlot Baits
plotDistFunPlot the Distance Function
readAndMergeRead And Merge
readSampleRead Sample
setExperimentSet Experiment
Chicago documentation built on May 2, 2018, 2:11 a.m.