$,GenomicInteractions-method
                        Quick access to GenomicInteractions metadata
                        columns
GenomicInteractions     Function to create a GenomicInteraction object
GenomicInteractions-class
                        A S4 class to represent interactions between
                        genomic regions.
GenomicInteractions-package
                        A package for looking at genomic interaction
                        data.
[                       Standard subsetting methods for
                        GenomicInteractions objects
annotateAnchors         Annotate anchors
annotateInteractions    Annotate the interactions in a
                        GenomicInteractions object
c                       Combine GenomicInteractions Methods
calculateDistances      Calculate interaction distances
capitalize              Capitalize first letter of string
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.
findOverlaps            Find overlaps between GRanges and
                        GenomicInteractions objects
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
length,GenomicInteractions-method
                        Get the length of a GenomicInteractions
                        GIObject
makeGenomicInteractionsFromFile
                        Function to create GenomicInteraction objects
                        from a file
mm9_refseq_promoters    Mouse Refseq promoters from chr 14-15
plotCisTrans            Plots the percentages of cis and trans
                        interactions for a GenomicInteractions 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 GenomicInteractions Object
plotInteractionAnnotations
                        Plot a donut plot of interaction types for an
                        annotated GenomicInteractions object
plotSummaryStats        Plot summary statistics for a
                        GenomicInteractions object
plotViewpoint           Plot coverage around a virtual 4C viewpoint
print,GenomicInteractions-method
                        Print function for GenomicInteractions
removeDups              Remove all but one occurences of a duplicated
                        interaction
resetAnnotations        Reset annotations made to a GenomicInteractions
                        object
sameStrand              Tests whether anchors have the same strand.
seqinfo,GenomicInteractions-method
                        Acessing/modifying sequence information for a
                        GenomicInteractions object
setters                 Functions to set data held in a
                        GenomicInteractions object.
show,GenomicInteractions-method
                        Representation function for GenomicInteractions
sort,GenomicInteractions-method
                        Sort GenomicInteractions Object
subsetByFeatures        Subset a GenomicInteractions object by features
sum,GenomicInteractions-method
                        Return the total number of interactions in a
                        GenomicInteractions GIObject
summariseByFeatures     Summary statistics of interactions for a given
                        feature set
trim,GenomicInteractions-method
                        Trim a GenomicInteractions object
viewPoint               Virtual 4C viewpoint
