# Differential Analyis of Hi-C Data

## Documentation for package ‘diffHic’ version 1.16.0

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

## Help Pages

$-method | pairParam class and methods
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
diffHic | View diffHic user's guide
diffHicUsersGuide | View diffHic user's guide
domainDirections | Calculate domain directionality
emptyGenome | Methods for processing DNase Hi-C data
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
filterTrended | Filtering strategies for bin pairs
getArea | Get interaction area
getPairData | Get read pair data
loadChromos | Load data from an index file
loadData | Load data from an index file
marginCounts | Collect marginal counts for each bin
matchMargins | Normalize CNV biases
mergeCMs | Merge ContactMatrix objects
mergePairs | Merge read pairs
neighborCounts | Load Hi-C interaction counts
normalizeCNV | Normalize CNV biases
pairParam | pairParam class and methods
pairParam-class | pairParam class and methods
plotDI | Construct a plaid plot of differential interactions
plotPlaid | Construct a plaid plot of interactions
preparePairs | Prepare Hi-C pairs
prepPseudoPairs | Methods for processing DNase Hi-C data
prunePairs | Prune read pairs
readMTX2IntSet | Create an InteractionSet from a BED file and Matrix Market files
reform | pairParam class and methods
reform-method | pairParam class and methods
rotDI | Construct a plaid plot of differential interactions
rotPlaid | Construct a plaid plot of interactions
savePairs | Save Hi-C read pairs
segmentGenome | Methods for processing DNase Hi-C data
show-method | pairParam class and methods
squareCounts | Load Hi-C interaction counts
totalCounts | Get the total counts