Learn R Programming

⚠️There's a newer version (3.7.2) of this package.Take me there.

CNVScope (version 2.9.2)

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.

Copy Link

Version

Install

install.packages('CNVScope')

Monthly Downloads

398

Version

2.9.2

License

BSD_3_clause + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

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

Maintainer

James Dalgleish

Last Published

December 5th, 2019

Functions in CNVScope (2.9.2)

underscored_pos_to_GRanges

Convert coordinates in underscored format to a GRanges object.

importBreakpointBed

Import a breakpoint BED file.

getInterchromosomalInteractivePlot

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

Server component of the CNVScope plotly shiny application.

rebinGenomicInteractions

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

writeAsymmetricMeltedChromosomalMatrixToDisk

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

postProcessLinRegMatrix

Postprocess linear regression matrix.

GRanges_to_underscored_pos

Convert GRanges object to underscord positions.

Create a linear regression matrix.

writeMeltedChromosomalMatrixToDisk

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

calcCNVKernelProbDist

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

averageMatrixEdges

Average edges of a matrix to facilitate downsampling.

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.

runCNVScopeLocal

Runs the CNVScope plotly shiny application.

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

createChromosomalMatrixSet

Create chromosomal interaction matrices for CNVScope shiny application.

runCNVScopeShiny

Runs the CNVScope plotly shiny application.

downsample_genomic_matrix

Rescale positive and negative data, preserving sign information.

Read GDC segmentation datafile for low-pass sequencing data.

extractNegLogPval

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

formSampleMatrixFromRawGDCData

Form sample matrix from GDC copy number data files.

getGlobalRescalingStats

Calculate several base statistics for color rescaling.

getBlockAverageMatrixFromBreakpoints

Calculate block averages and areas in a matrix given breakpoints.

Rescale positive and negative data, preserving sign information.