annotatePairs           Annotate bin pairs
boxPairs                Put bin pairs into boxes
clusterPairs            Cluster bin pairs
compartmentalize        Identify genomic compartments
connectCounts           Count connecting read pairs
consolidatePairs        Consolidate results for interactions
correctedContact        Iterative correction of Hi-C counts
cutGenome               Cut up the genome
diClusters              Cluster significant bin pairs to DIs
diffHicUsersGuide       View diffHic user's guide
domainDirections        Calculate domain directionality
enrichedPairs           Collect local enrichment statistics for bin
                        pairs
extractPatch            Extract a patch of the interaction space
filterDiag              Filtering of diagonal bin pairs
filterDirect            Filtering strategies for bin pairs
filterPeaks             Filter bin pairs for likely peaks
getArea                 Get interaction area
getPairData             Get read pair data
loadData                Load data from an index file
marginCounts            Collect marginal counts for each bin
mergeCMs                Merge ContactMatrix objects
mergePairs              Merge read pairs
neighborCounts          Load Hi-C interaction counts
normalizeCNV            Normalize CNV biases
pairParam               pairParam class and methods
plotDI                  Construct a plaid plot of differential
                        interactions
plotPlaid               Construct a plaid plot of interactions
prepPseudoPairs         Methods for processing DNase Hi-C data
preparePairs            Prepare Hi-C pairs
prunePairs              Prune read pairs
readMTX2IntSet          Create an InteractionSet from a BED file and
                        Matrix Market files
savePairs               Save Hi-C read pairs
squareCounts            Load Hi-C interaction counts
totalCounts             Get the total counts
