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CNVScope (version 3.7.2)

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

Description

Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.

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Install

install.packages('CNVScope')

Monthly Downloads

398

Version

3.7.2

License

BSD_3_clause + file LICENSE

Issues

0

Pull Requests

0

Stars

8

Forks

3

Maintainer

James Dalgleish

Last Published

March 30th, 2022

Functions in CNVScope (3.7.2)

importBreakpointBed

Import a breakpoint BED file.
nbl_result_matrix_sign_small

Neuroblastoma sample CNV relationship matrix
createChromosomalMatrixSet

Create chromosomal interaction matrices for CNVScope shiny application.
extractNegLogPval

Find the negative log p-value of a pair of vectors.
formSampleMatrixFromRawGDCData

Form sample matrix from GDC copy number data files.
calcVecLMs

Create a linear regression matrix.
mathead

Gets a small piece of a matrix (top left corner) for viewing, rather than pulling the first n rows.
writeMeltedChromosomalMatrixToDisk

Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.
getInterchromosomalInteractivePlot

Create an HTML widget for use in shiny or webshot for a given pair of chromosomes.
getGlobalRescalingStats

Calculate several base statistics for color rescaling.
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.
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.
runCNVScopeLocal

Runs the CNVScope plotly shiny application.
rebinGenomicInteractions

Assign GenomicInteractions to a predefined series of bins for row and column, corresponding to a genomic matrix.
postProcessLinRegMatrix

Postprocess linear regression matrix.
divisors

List of Divisors
downsample_genomic_matrix

Rescale positive and negative data, preserving sign information.
getAsymmetricBlockIndices

Get Block Indices from an asymmetric (or symmetric) matrix.
runCNVScopeShiny

Runs the CNVScope plotly shiny application.
signedRescale

Rescale positive and negative data, preserving sign information.
getBlockAverageMatrixFromBreakpoints

Calculate block averages and areas in a matrix given breakpoints.
CNVScopeserver

Server component of the CNVScope plotly shiny application.
averageMatrixEdges

Average edges of a matrix to facilitate downsampling.
GRanges_to_underscored_pos

Convert GRanges object to underscord positions.
calcCNVKernelProbDist

Calculate the probability distribution of CNV concordance events with a fast kernel