InteractionArray-class
                        InteractionArray Class
InteractionJaggedArray-class
                        InteractionJaggedArray Class
InteractionMatrix-class
                        InteractionMatrix Class
JaggedArray-class       JaggedArray Class
MatrixSelection-class   MatrixSelection Class
MergedGInteractions-class
                        MergedGInteractions Class
aggHicMatrices          Aggregate count matrices from InteractionArray
                        objects
aggMetadata             Aggregate the metadata columns of merged pairs
as_ginteractions        Convert DataFrames to GInteraction objects
assignToBins            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.
clusters                Get clustered pairs from MergedGInteractions
                        object
counts,InteractionArray-method
                        Access count matrices from InteractionArray or
                        InteractionMatrix
defaultBuffer           Return default buffer If InteractionArray is
                        supplied, it uses the dimensions of counts
                        matrices to set the buffer dimensions.
findOverlaps            Overlap methods for InteractionJaggedArray
hdf5BlockApply          HDF5-backed blockApply
makeRandomGRanges       Creating random GRanges & GInteractions
mariner-package         Mariner: Explore the Hi-Cs
mergePairs              Merge sets of paired interactions
path,InteractionMatrix-method
                        Accessor for h5File path from an
                        InteractionMatrix
pileupBoundaries        Pileup Hi-C contacts around boundary regions
pileupDomains           Pileup Hi-C domains
pileupPixels            Pileup Hi-C pixels
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
regularize              Regularize JaggedArray or
                        InteractionJaggedArray objects
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
sets                    Get each set from a MergedGInteractions object
shiftRanges             Flexibly shifting GRanges according to strand
snapToBins              Snap GRanges or GInteractions to nearest bins
sources                 Accessor for sources
