Differential Analyis of Hi-C Data

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Documentation for package ‘diffHic’ version 1.30.0

• 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