Differential Analyis of Hi-C Data


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Documentation for package ‘diffHic’ version 1.28.0

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$-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