A/B compartment detection and differential analysis

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Documentation for package ‘HiCDOC’ version 1.11.1

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

Help Pages

HiCDOC-package	A/B compartment detection and differential analysis
chromosomes	Methods to access a 'HiCDOCDataSet' components.
chromosomes-method	Methods to access a 'HiCDOCDataSet' components.
compartments	Methods to access a 'HiCDOCDataSet' components.
compartments-method	Methods to access a 'HiCDOCDataSet' components.
concordances	Methods to access a 'HiCDOCDataSet' components.
concordances-method	Methods to access a 'HiCDOCDataSet' components.
defaultHiCDOCParameters	Access the parameters of a 'HiCDOCDataSet'.
detectCompartments	A and B compartments detection and differences across conditions.
differences	Methods to access a 'HiCDOCDataSet' components.
differences-method	Methods to access a 'HiCDOCDataSet' components.
exampleHiCDOCDataSet	Example HiCDOCDataSet.
exampleHiCDOCDataSetProcessed	Example HiCDOCDataSet, filtered, normalized and with compartements detected.
filterSmallChromosomes	Filter small chromosomes.
filterSparseReplicates	Filter sparse replicates.
filterWeakPositions	Filter weak positions.
HiCDOC	Default pipeline to run on the HiCDOC analysis.
HiCDOCDataSet	'HiCDOCDataSet' S4 class.
HiCDOCDataSet-class	'HiCDOCDataSet' S4 class.
HiCDOCDataSet-methods	Methods to access a 'HiCDOCDataSet' components.
HiCDOCDataSet-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.
normalizeBiologicalBiases	Normalize biological biases.
normalizeDistanceEffect	Normalize distance effect.
normalizeTechnicalBiases	Normalize technical biases.
parameters	Access the parameters of a 'HiCDOCDataSet'.
parameters-method	Access the parameters of a 'HiCDOCDataSet'.
parameters<-	Access the parameters of a 'HiCDOCDataSet'.
parameters<--method	Access the parameters of a 'HiCDOCDataSet'.
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'.
sampleConditions	Methods to access a 'HiCDOCDataSet' components.
sampleConditions-method	Methods to access a 'HiCDOCDataSet' components.
sampleReplicates	Methods to access a 'HiCDOCDataSet' components.
sampleReplicates-method	Methods to access a 'HiCDOCDataSet' components.
show-method	Methods to access a 'HiCDOCDataSet' components.