$-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 | Compute local enrichment 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 |
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 |