# A/B compartment detection and differential analysis

## Documentation for package ‘HiCDOC’ version 1.0.0

- 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.
_PACKAGE | A/B compartment detection and differential analysis