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

## Documentation for package ‘CNVScope’ version 3.1.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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.
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.