copynumber

DOI: 10.18129/B9.bioc.copynumber    

Segmentation of single- and multi-track copy number data by penalized least squares regression.

Bioconductor version: Release (3.15)

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

Author: Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.

Maintainer: Gro Nilsen <gronilse at ifi.uio.no>

Installation

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

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

BiocManager::install("copynumber")

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("copynumber")

 

PDF	R Script	copynumber.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Genetics, SNP, Software, Visualization, aCGH
Version	1.36.0
In Bioconductor since	BioC 2.12 (R-3.0) (9.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics
Imports	S4Vectors, IRanges, GenomicRanges
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	sequenza
Suggests Me	PureCN
Links To Me
Build Report

Package Archives

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

Source Package	copynumber_1.36.0.tar.gz
Windows Binary
macOS Binary (x86_64)	copynumber_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/copynumber
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/copynumber
Package Short Url	https://bioconductor.org/packages/copynumber/
Package Downloads Report	Download Stats