To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNAnorm")

In most cases, you don't need to download the package archive at all.

CNAnorm

   

A normalization method for Copy Number Aberration in cancer samples

Bioconductor version: 3.2

Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.

Author: Stefano Berri <sberri at illumina.com>, Henry M. Wood <H.M.Wood at leeds.ac.uk>, Arief Gusnanto <a.gusnanto at leeds.ac.uk>

Maintainer: Stefano Berri <sberri at illumina.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CNAnorm")

Documentation

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

browseVignettes("CNAnorm")

 

PDF CNAnorm.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Coverage, DNASeq, GenomicVariation, Normalization, Sequencing, Software, WholeGenome
Version 1.16.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License GPL-2
Depends R (>= 2.10.1), methods
Imports DNAcopy
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://www.r-project.org
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source CNAnorm_1.16.0.tar.gz
Windows Binary CNAnorm_1.16.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CNAnorm_1.16.0.tgz
Mac OS X 10.9 (Mavericks) CNAnorm_1.16.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CNAnorm/tree/release-3.2
Package Short Url http://bioconductor.org/packages/CNAnorm/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center