.getRunsAndTotals       A helper function for getRunTotals
bigBinSize              Big bin size
binSummarizedExperiment
                        Bin a Summarized experiment into a set of bins
                        given by a GRanges object
binnedDeltaPlot         Plot of Binned Delta Counts
binnedDeltaSE           Binned difference of mean capture-C counts
                        between EScells and Neurons
binnedSummarizedExperiment
                        Binned Capture-C counts of EScells and Neurons
deltaSE                 Difference of mean capture-C counts between
                        EScells and Neurons
downshiftDFtoMatrix     Downshift from DF to matrix
generatePermutation     Generate permutation for permutation testing
getDeltaSE              Make delta summarized experiment:
getLopsidedness         Get the lopsidedness statistic
getMeanNormalizedCountsSE
                        Make mean treatment summarized experiment:
getNormalizedCountsSE   Get normalized counts
getOverlapWeights       Get the binning factors for one set of GRanges
                        into another
getPValueCutoff         This function returns the significance levels
                        for min, max, "abs" and lopsidedness.
getRunAndLopsidednessStatistics
                        Get the distribution of run and lopsidedness
                        statistics
getRunStatistics        This function is called by
                        getRunsStatisticsDist on the individual
                        elements of a list of scrambled runs.
getRunStatisticsDist    This takes a list of (scrambled) runs and
                        returns their run statistics
getRunTotals            Get the runs and their values
getSignificantRegions   Get ths significant regions from delta data
getSizeFactorsDF        Get the size factors for count normalization
getSizeFactorsSE        Get the size factors for SummarizedExperiment
miniDeltaSE             Difference of mean capture-C counts between
                        EScells and Neurons
miniSE                  Capture-C counts of EScells and Neurons
miniSEDF                Capture-C counts of EScells and Neurons
numPermutations         Number of permutations used in example
                        permutation testing.
pValue                  P-value
plotSignificantRegions
                        This produces a plot of the region of interest
                        showing regions of significance.
plotTitle               Title for delta capture-C plot
rebinToMultiple         Rebin a SummarizedExperiment to a multiple of
                        its bin width
regionOfInterest        Region of interest surrounding the viewpoint
significanceType        Type for testing significance
significantRegions      Regions of significant remodeling in example
                        data
significantRegionsPlot
                        A plot of the significant regions in the sample
                        data.
smallBinSize            Small Bin Size
smallBins               Small Bins
smallSetOfSmallBins     Small Bins
smallerDeltaSE          A subset of miniDeltaSE.
viewpointRegion         Region surrounding the viewpoint
weightsExampleBins      Weights example bins
weightsExampleGr        Weights example
