Differential analyis of Hi-C data

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Documentation for package ‘diffHic’ version 1.0.1

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$ 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