.importHicLib           Function to read in processed Hi-C interaction
                        data generated by hiclib
.importHomer            Function to read in processed Hi-C interaction
                        data generated by HOMER
.processChiapetName     Function to process names relating to
                        interactions stored in bed12 formats.
.readBam                Function to read in interaction-data stored in
                        a BAM file
.readTwoBams            Function to read in interaction-data stored in
                        a pair of BAM files
.validateInput          Function to validate tabular input
GenomicInteractions     Function to create a GenomicInteractions object
GenomicInteractions-class
                        A S4 class to represent interactions between
                        genomic regions.
GenomicInteractions-package
                        GenomicInteractions
InteractionTrack        Constructor to create an InteractionTrack
                        object
InteractionTrack-class
                        A class to hold chromatin interaction data for
                        a specific genomic region
annotateInteractions    Annotate the interactions in a GInteractions
                        object
annotateRegions         Annotate regions
asBED,GInteractions-method
                        Coerce to BED structure
availableDisplayPars    The default display parameters for a track
                        object class can be queries using the
                        availableDisplayPars function.
calculateDistances      Calculate interaction distances
categoriseInteractions
                        Get the numbers of interaction types existing
                        in your data
countsBetweenAnchors    Summarise interactions between defined anchors
export.bed12            Export interactions in BED12 format.
export.bedpe            Export interactions in BED Paired-End format.
export.chiasig          Export interactions in a BEDPE-like format for
                        use with ChiaSig
export.igraph           Export interactions to an igraph object.
get_binom_ligation_threshold
                        get self ligation threshold with binomial test
get_self_ligation_threshold
                        Get self ligation threshold with SD method from
                        Heidari et al
getters                 Functions to access data held in a
                        GenomicInteractions object.
hg19.refseq.transcripts
                        Human Refseq transcripts from chr 17-18
hic_example_data        Example HiC dataset
is.pp                   Interaction Type Helpers
makeGenomicInteractionsFromFile
                        Function to create GenomicInteraction objects
                        from a file
mm9_refseq_promoters    Mouse Refseq promoters from chr 14-15
plotAvgViewpoint        Plot coverage around a set of virtual 4C
                        viewpoints
plotCisTrans            Plots the percentages of cis and trans
                        interactions for a GInteractions object as a
                        donut plot.
plotCounts              Plot a bar chart of the number of interactions
                        supported by different numbers of reads in your
                        data.
plotDists               Plots a histogram of interaction distances for
                        a GInteractions Object
plotInteractionAnnotations
                        Plot a donut plot of interaction types for an
                        annotated GInteractions object
plotSummaryStats        Plot summary statistics for a GInteractions
                        object
plotViewpoint           Plot coverage around a virtual 4C viewpoint
removeDups              Remove all but one occurences of a duplicated
                        interaction
resetAnnotations        Reset annotations made to a GInteractions
                        object
sameStrand              Tests whether anchors have the same strand.
setters                 Functions to set data held in a GInteractions
                        object.
subsetByFeatures        Subset a GInteractions object by features
sum,GInteractions-method
                        Return the total number of interactions in a
                        GInteractions GIObject
summariseByFeaturePairs
                        Summarise the number of interactions between
                        two sets of features.
summariseByFeatures     Summary statistics of interactions for a given
                        feature set
thymus_enh              Putative enhancers from mouse thymus data
updateObject,GenomicInteractions-method
                        updateObject method for GenomicInteractions
                        1.3.7 and earlier
viewPoint               Virtual 4C viewpoint
