CNVMetrics

DOI: 10.18129/B9.bioc.CNVMetrics    

Copy Number Variant Metrics

Bioconductor version: Release (3.15)

The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.

Author: Astrid DeschĂȘnes [aut, cre] , Pascal Belleau [aut] , David A. Tuveson [aut], Alexander Krasnitz [aut]

Maintainer: Astrid DeschĂȘnes <adeschen at hotmail.com>

Citation (from within R, enter citation("CNVMetrics")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CNVMetrics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CNVMetrics")

 

HTML R Script Copy number variant metrics
PDF   Reference Manual
Text   NEWS

Details

biocViews BiologicalQuestion, CopyNumberVariation, Software
Version 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1)
Imports GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/krasnitzlab/CNVMetrics https://krasnitzlab.github.io/CNVMetrics/
BugReports https://github.com/krasnitzlab/CNVMetrics/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CNVMetrics_1.0.0.tar.gz
Windows Binary CNVMetrics_1.0.0.zip
macOS 10.13 (High Sierra) CNVMetrics_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CNVMetrics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CNVMetrics
Package Short Url https://bioconductor.org/packages/CNVMetrics/
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