All functions

HiCDOC-package

A/B compartment detection and differential analysis

HiCDOC()

Default pipeline to run on the HiCDOC analysis.

HiCDOCDataSet-class

HiCDOCDataSet S4 class.

chromosomes() positions() conditions() replicates() interactions() binSize() compartments() differences() concordances()

Methods to access a HiCDOCDataSet components.

defaultHiCDOCParameters parameters() `parameters<-`()

Access the parameters of a HiCDOCDataSet.

HiCDOCDataSetFromCool()

HiCDOCDataSet constructor from Cool files.

HiCDOCDataSetFromHiC()

HiCDOCDataSet constructor from HiC files.

HiCDOCDataSetFromHiCPro()

HiCDOCDataSet constructor from HiC-Pro files.

HiCDOCDataSetFromTabular()

HiCDOCDataSet constructor from a tabular file.

detectCompartments()

A and B compartments detection and differences across conditions.

exampleHiCDOCDataSet

Example HiCDOCDataSet.

exampleHiCDOCDataSetProcessed

Example HiCDOCDataSet, filtered and normalized.

filterSmallChromosomes()

Filter small chromosomes.

filterSparseReplicates()

Filter sparse replicates.

filterWeakPositions()

Filter weak positions.

normalizeBiologicalBiases()

Normalize biological biases.

normalizeDistanceEffect()

Normalize distance effect.

normalizeTechnicalBiases()

Normalize technical biases.

plotCentroids()

Plot centroids.

plotCompartmentChanges()

Plot compartment changes.

plotCompartments()

Plot A/B compartments.

plotConcordanceDifferences()

Plot the distribution of concordance differences.

plotConcordances()

Plot concordances.

plotDistanceEffect()

Plot the distance effect.

plotInteractions()

Plot interaction matrices.

plotSelfInteractionRatios()

Plot boxplots of self interaction ratios.

reduceHiCDOCDataSet()

Reduce a HiCDOCDataSet.