CNVScopeserver          Server component of the CNVScope plotly shiny
                        application.
GRanges_to_underscored_pos
                        Convert GRanges object to underscord positions.
averageMatrixEdges      Average edges of a matrix to facilitate
                        downsampling.
calcCNVKernelProbDist   Calculate the probability distribution of CNV
                        concordance events with a fast kernel
calcVecLMs              Create a linear regression matrix.
createChromosomalMatrixSet
                        Create chromosomal interaction matrices for
                        CNVScope shiny application.
divisors                List of Divisors
downsample_genomic_matrix
                        Rescale positive and negative data, preserving
                        sign information.
extractNegLogPval       Find the negative log p-value of a pair of
                        vectors.
formSampleMatrixFromRawGDCData
                        Form sample matrix from GDC copy number data
                        files.
freadGDCfile            Read GDC segmentation datafile for low-pass
                        sequencing data.
getAnnotationMatrix     Get the genes in the genomic ranges indicated
                        by the row and column labels.
getAsymmetricBlockIndices
                        Get Block Indices from an asymmetric (or
                        symmetric) matrix.
getBlockAverageMatrixFromBreakpoints
                        Calculate block averages and areas in a matrix
                        given breakpoints.
getGlobalRescalingStats
                        Calculate several base statistics for color
                        rescaling.
getInterchromosomalInteractivePlot
                        Create an HTML widget for use in shiny or
                        webshot for a given pair of chromosomes.
importBreakpointBed     Import a breakpoint BED file.
mathead                 Gets a small piece of a matrix (top left
                        corner) for viewing, rather than pulling the
                        first n rows.
nbl_result_matrix_sign_small
                        Neuroblastoma sample CNV relationship matrix
postProcessLinRegMatrix
                        Postprocess linear regression matrix.
rebinGenomicInteractions
                        Assign GenomicInteractions to a predefined
                        series of bins for row and column,
                        corresponding to a genomic matrix.
runCNVScopeLocal        Runs the CNVScope plotly shiny application.
runCNVScopeShiny        Runs the CNVScope plotly shiny application.
signedRescale           Rescale positive and negative data, preserving
                        sign information.
underscored_pos_to_GRanges
                        Convert coordinates in underscored format to a
                        GRanges object.
writeAsymmetricMeltedChromosomalMatrixToDisk
                        Write a matrix, with genes, of a submatrix of a
                        whole genome interaction matrix to disk.
writeMeltedChromosomalMatrixToDisk
                        Write a matrix, with genes, of a submatrix of a
                        whole genome interaction matrix to disk.
