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CNVScope (version 2.9.4)

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

253

Version

2.9.4

License

BSD_3_clause + file LICENSE

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Repository

https://github.com/jamesdalg/CNVScope/

Maintainer

James Dalgleish

Last Published

December 7th, 2019

Functions in CNVScope (2.9.4)

GRanges_to_underscored_pos

Convert GRanges object to underscord positions.

Server component of the CNVScope plotly shiny application.

postProcessLinRegMatrix

Postprocess linear regression matrix.

rebinGenomicInteractions

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

getBlockAverageMatrixFromBreakpoints

Calculate block averages and areas in a matrix given breakpoints.

averageMatrixEdges

Average edges of a matrix to facilitate downsampling.

getGlobalRescalingStats

Calculate several base statistics for color rescaling.

calcCNVKernelProbDist

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

extractNegLogPval

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

downsample_genomic_matrix

Rescale positive and negative data, preserving sign information.

getInterchromosomalInteractivePlot

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

importBreakpointBed

Import a breakpoint BED file.

getAsymmetricBlockIndices

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

getAnnotationMatrix

Get the genes in the genomic ranges indicated by the row and column labels.

Rescale positive and negative data, preserving sign information.

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

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.

runCNVScopeLocal

Runs the CNVScope plotly shiny application.

runCNVScopeShiny

Runs the CNVScope plotly shiny application.

underscored_pos_to_GRanges

Convert coordinates in underscored format to a GRanges object.

createChromosomalMatrixSet

Create chromosomal interaction matrices for CNVScope shiny application.

formSampleMatrixFromRawGDCData

Form sample matrix from GDC copy number data files.

Create a linear regression matrix.

Read GDC segmentation datafile for low-pass sequencing data.