A/B compartment detection and differential analysis


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Documentation for package ‘HiCDOC’ version 1.4.0

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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