Package: CNAnorm 1.59.0

Stefano Berri

CNAnorm: A normalization method for Copy Number Aberration in cancer samples

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.

Authors:Stefano Berri <[email protected]>, Henry M. Wood <[email protected]>, Arief Gusnanto <[email protected]>

CNAnorm_1.59.0.tar.gz
CNAnorm_1.59.0.zip(r-4.7)CNAnorm_1.59.0.zip(r-4.6)CNAnorm_1.59.0.zip(r-4.5)
CNAnorm_1.59.0.tgz(r-4.6-x86_64)CNAnorm_1.59.0.tgz(r-4.6-arm64)CNAnorm_1.59.0.tgz(r-4.5-x86_64)CNAnorm_1.59.0.tgz(r-4.5-arm64)
CNAnorm_1.59.0.tar.gz(r-4.7-arm64)CNAnorm_1.59.0.tar.gz(r-4.7-x86_64)CNAnorm_1.59.0.tar.gz(r-4.6-arm64)CNAnorm_1.59.0.tar.gz(r-4.6-x86_64)
CNAnorm_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNAnorm/json (API)

# Install 'CNAnorm' in R:

install.packages('CNAnorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CN - A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.
gPar - An object with the default graphical parameters
hg19_hs_ideogr - An object with the ideogram information for homo sapiens - hg19
LS041 - Mapped reads in tumor and matched blood for patient LS041

On BioConductor:CNAnorm-1.59.0(bioc 3.24)CNAnorm-1.58.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

copynumbervariation sequencing coverage normalization wholegenome dnaseq genomicvariation

4.30 score 9 scripts 21 mentions 26 exports 1 dependencies

Last updated from:48ad80c66d. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	137
linux-devel-arm64	NOTE	146
linux-devel-x86_64	NOTE	143
source / vignettes	OK	164
linux-release-arm64	NOTE	133
linux-release-x86_64	NOTE	194
macos-release-arm64	NOTE	88
macos-release-x86_64	NOTE	261
macos-oldrel-arm64	NOTE	143
macos-oldrel-x86_64	NOTE	165
windows-devel	NOTE	90
windows-release	NOTE	86
windows-oldrel	NOTE	91
wasm-release	OK	98

Exports:addDNACopy addSmooth arms chrs chrs<-CNAnormWorkflow dataFrame2object discreteNorm exportTable gcNorm peakPloidy plotGenome plotPeaks pos pos<-ratio ratio.n ratio.s ratio.s.n segMean segMean.n sugg.peaks sugg.ploidy valid.peaks valid.ploidy validation

Dependencies:DNAcopy

An introduction to CNAnorm

Rendered fromCNAnorm.Snwusingutils::Sweave

Last update: 2014-03-05
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Methods for Function addDNACopy in Package `CNAnorm'	addDNACopy addDNACopy,CNAnorm-method addDNACopy-methods
Methods for Function addSmooth in Package `CNAnorm'	addSmooth addSmooth,CNAnorm-method addSmooth-methods
Accessors methods for Function ratio in Package `CNAnorm'	arms arms,CNAnorm-method arms-methods chrs chrs-methods chrs<- chrs<--methods pos pos,CNAnorm-method pos-methods pos<- pos<--methods
A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.	CN
Class "CNAnorm"	chrs,CNAnorm-method chrs<-,CNAnorm-method CNAnorm CNAnorm-class length,CNAnorm-method pos<-,CNAnorm-method ratio,CNAnorm-method ratio.n,CNAnorm-method ratio.s,CNAnorm-method ratio.s.n,CNAnorm-method segMean,CNAnorm-method segMean.n,CNAnorm-method sugg.peaks,CNAnorm-method sugg.ploidy,CNAnorm-method valid.peaks,CNAnorm-method valid.ploidy,CNAnorm-method [,CNAnorm-method
Wrapper to '"CNAnorm"' workflow	CNAnormWorkflow
Convert a data frame into an object of Class '"CNAnorm"'	dataFrame2object
Class "DerivData"	DerivData-class length,DerivData-method
Methods for Function addSmooth in Package `CNAnorm'	discreteNorm discreteNorm,CNAnorm-method discreteNorm-methods
Methods for Function exportTable in Package `CNAnorm'	exportTable exportTable,CNAnorm-method exportTable-methods
Methods for Function gcNorm in Package `CNAnorm'	gcNorm gcNorm,CNAnorm-method gcNorm-methods
An object with the default graphical parameters	gPar
An object with the ideogram information for homo sapiens - hg19	hg19_hs_ideogr
Class "InData" ~~~	InData-class length,InData-method
Mapped reads in tumor and matched blood for patient LS041	LS041
Class "Params"	Params-class
Methods for Function peakPloidy in Package `CNAnorm'	peakPloidy peakPloidy,CNAnorm-method peakPloidy-methods
Methods for Function plotGenome in Package `CNAnorm'	plotGenome plotGenome,CNAnorm-method plotGenome-methods
Methods for Function plotPeaks in Package `CNAnorm'	plotPeaks plotPeaks,CNAnorm-method plotPeaks-methods
Methods for Function ratio in Package `CNAnorm'	ratio ratio-methods ratio.n ratio.n-methods ratio.s ratio.s-methods ratio.s.n ratio.s.n-methods segMean segMean-methods segMean.n segMean.n-methods
Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm'	sugg.peaks sugg.peaks-methods sugg.ploidy sugg.ploidy-methods valid.peaks valid.peaks-methods valid.ploidy valid.ploidy-methods
Methods for Function addSmooth in Package `CNAnorm'	validation validation,CNAnorm-method validation-methods