A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization


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Documentation for package ‘CNVScope’ version 3.5.6

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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.
CNVScopeserver Server component of the CNVScope plotly shiny application.
createChromosomalMatrixSet Create chromosomal interaction matrices for CNVScope shiny application.
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.
GRanges_to_underscored_pos Convert GRanges object to underscord positions.
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.