# Differential analyis of Hi-C data

## Documentation for package ‘diffHic’ version 1.0.1

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

## Help Pages

$ | DIList class and methods
$-method | DIList class and methods
$-method | pairParam class and methods
anchors | DIList class and methods
anchors-method | DIList class and methods
asDGEList | DIList class and methods
asDGEList-method | DIList class and methods
boxPairs | Put bin pairs into boxes
c-method | DIList class and methods
clusterPairs | Cluster bin pairs
colData | DIList class and methods
colData-method | DIList class and methods
connectCounts | Count connecting read pairs
consolidatePairs | Consolidate results for bin pairs
correctedContact | Iterative correction of Hi-C counts
counts | DIList class and methods
counts-method | DIList class and methods
cutGenome | Cut up the genome
diffHic | View diffHic user's guide
diffHicUsersGuide | View diffHic user's guide
DIList | DIList class and methods
DIList-class | DIList class and methods
dim-method | DIList class and methods
dimnames-method | DIList class and methods
enrichedPairs | Compute local enrichment for bin pairs
exptData | DIList class and methods
exptData-method | DIList class and methods
filterDirect | Filtering strategies for bin pairs
filterPeaks | Filter bin pairs for likely peaks
filterTrended | Filtering strategies for bin pairs
getArea | Get interaction area
getDistance | Get the linear distance for each interaction
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
mergePairs | Merge read pairs
normalize | DIList class and methods
normalize-method | DIList class and methods
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
reform | pairParam class and methods
reform-method | pairParam class and methods
regions | DIList class and methods
regions-method | DIList class and methods
rotDI | Construct a plaid plot of differential interactions
rotPlaid | Construct a plaid plot of interactions
savePairs | Save Hi-C interactions
segmentGenome | Methods for processing DNase Hi-C data
show-method | DIList class and methods
show-method | pairParam class and methods
squareCounts | Load Hi-C interaction counts
targets | DIList class and methods
targets-method | DIList class and methods
totalCounts | Get the total counts
[-method | DIList class and methods