A/B compartment detection and differential analysis

Documentation for package ‘HiCDOC’ version 1.15.1

detectCompartments	A and B compartments detection and differences across conditions.
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.