GenomicInteractions     Function to create GenomicInteraction objects.
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
calculateDistances      Calculate interaction distances
capitalize              Capitalize first letter of string
categoriseInteractions
                        Get the numbers of interaction types existing
                        in your data
export.bed12            Export interactions in BED12 format.
export.bedpe            Export interactions in BED Paired-End format.
export.igraph           Export interactions to an igraph object.
findOverlaps            Find overlaps between a GRanges and a
                        GenomicInteractions object
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
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
plotRegion              Plot interactions within a specified region.
plotSummaryStats        Plot summary statistics for a
                        GenomicInteractions object
print,GenomicInteractions-method
                        Print function for GenomicInteractions
resetAnnotations        Reset annotations made to a GenomicInteractions
                        object
setters                 Functions to set data held in a
                        GenomicInteractions object.
show,GenomicInteractions-method
                        Representation function for GenomicInteractions
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
viewPoint               Plot coverage of interactions originating at a
                        given viewpoint.
viewPointAverage        Plot coverage of interactions originating at a
                        given set of viewpoints.
