InteractionArray-class
                        InteractionArray Class
InteractionMatrix-class
                        InteractionMatrix Class
MatrixSelection-class   MatrixSelection Class
MergedGInteractions-class
                        MergedGInteractions Class
aggHicMatrices          Aggregate count matrices from InteractionArray
                        objects
aggPairMcols            Aggregate the metadata columns of merged pairs
as_ginteractions        Convert DataFrames to GInteraction objects
binPairs                Flexibly bin paired ranges
binRanges               Flexibly bin ranges
calcLoopEnrichment      Calculate loop enrichment over background.
changePixelRes          Change pixels from one resolution to another
                        selecting the new pixel using Hi-C data.
counts,InteractionArray-method
                        Access count matrices from InteractionArray or
                        InteractionMatrix
getPairClusters         Get clustered pairs from MergedGInteractions
                        object
hdf5BlockApply          HDF5-backed blockApply
mariner-package         Mariner: Explore the Hi-Cs
mergePairs              Merge sets of paired interactions
path,InteractionMatrix-method
                        Accessor for h5File path from an
                        InteractionMatrix
pixelsToMatrices        Expand pixels to submatrices
plotEnrichment          Adjust loop enrichment to remove distance-
                        dependent effect.
plotMatrix              Plot matrix
pullHicMatrices         Pull submatrices from '.hic' files
pullHicPixels           Pull contact frequency from '.hic' files
removeShortPairs        Remove interactions that would cross the Hi-C
                        diagonal or a specified distance from the
                        diagonal.
selectPixel             Get the pixel representing the strongest or
                        weakest interaction in an InteractionArray
selectRadius            Visualize selection for a MatrixSelection
                        object
selectionMethod         Get selectionMethod from MergedGInteractions
                        object
seqnames1               Access each portion of a GInteractions-like
                        object
shiftRanges             Flexibly shifting GRanges according to strand
snapToBins              Snap GRanges or GInteractions to nearest bins
sources                 Accessor for sources
subsetBySource          Subset MergedGInteractions by source
