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

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Documentation for package ‘CNVScope’ version 3.7.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.
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.
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.