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CNVScope (version 3.0.6)

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

3.0.6

License

BSD_3_clause + file LICENSE

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Repository

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

Maintainer

James Dalgleish

Last Published

April 27th, 2020

Functions in CNVScope (3.0.6)

rebinGenomicInteractions

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

Server component of the CNVScope plotly shiny application.

extractNegLogPval

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

GRanges_to_underscored_pos

Convert GRanges object to underscord positions.

writeMeltedChromosomalMatrixToDisk

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

postProcessLinRegMatrix

Postprocess linear regression matrix.

createChromosomalMatrixSet

Create chromosomal interaction matrices for CNVScope shiny application.

getBlockAverageMatrixFromBreakpoints

Calculate block averages and areas in a matrix given breakpoints.

nbl_result_matrix_sign_small

Neuroblastoma sample CNV relationship matrix

getAsymmetricBlockIndices

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

Create a linear regression matrix.

averageMatrixEdges

Average edges of a matrix to facilitate downsampling.

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

runCNVScopeShiny

Runs the CNVScope plotly shiny application.

getAnnotationMatrix

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

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.

Rescale positive and negative data, preserving sign information.

underscored_pos_to_GRanges

Convert coordinates in underscored format to a GRanges object.

importBreakpointBed

Import a breakpoint BED file.

runCNVScopeLocal

Runs the CNVScope plotly shiny application.

calcCNVKernelProbDist

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

formSampleMatrixFromRawGDCData

Form sample matrix from GDC copy number data files.

Read GDC segmentation datafile for low-pass sequencing data.

writeAsymmetricMeltedChromosomalMatrixToDisk

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

downsample_genomic_matrix

Rescale positive and negative data, preserving sign information.