CNAnorm: A normalization method for Copy Number Aberration in cancer samples
Version 1.22.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorStefano Berri <sberri@illumina.com>, Henry M. Wood <H.M.Wood@leeds.ac.uk>, Arief Gusnanto <a.gusnanto@leeds.ac.uk>
Bioconductor views CopyNumberVariation Coverage DNASeq GenomicVariation Normalization Sequencing WholeGenome
Date of publicationNone
MaintainerStefano Berri <sberri@illumina.com>
LicenseGPL-2
Version1.22.1
URL http://www.r-project.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNAnorm")

Man pages

addDNACopy-methods: Methods for Function addDNACopy in Package 'CNAnorm'
addSmooth-methods: Methods for Function addSmooth in Package 'CNAnorm'
chrsAndpos-methods: Accessors methods for Function ratio in Package 'CNAnorm'
CN: A CNAnorm object with information about most abundant ploidy...
CNAnorm-class: Class "CNAnorm"
dataFrame2object: Convert a data frame into an object of Class '"CNAnorm"'
data-hg19_hs_ideogr: An object with the ideogram information for homo sapiens -...
DerivData-class: Class "DerivData"
discreteNorm-methods: Methods for Function addSmooth in Package 'CNAnorm'
exportTable-method: Methods for Function exportTable in Package 'CNAnorm'
gcNorm-methods: Methods for Function gcNorm in Package 'CNAnorm'
gPar: An object with the default graphical parameters
InData-class: Class "InData" ~~~
LS041: Mapped reads in tumor and matched blood for patient LS041
Params-class: Class "Params"
peakPloidy: Methods for Function peakPloidy in Package 'CNAnorm'
plotGenome-methods: Methods for Function plotGenome in Package 'CNAnorm'
plotPeaks-methods: Methods for Function plotPeaks in Package 'CNAnorm'
ratio-methods: Methods for Function ratio in Package 'CNAnorm'
suggValid-methods: Methods for Function to retrieve suggested/validated ploidy...
validation-methods: Methods for Function addSmooth in Package 'CNAnorm'
workflowWrapper: Wrapper to '"CNAnorm"' workflow

Functions

CN Man page
CNAnorm Man page
CNAnorm-class Man page
CNAnormWorkflow Man page Source code
DerivData-class Man page
InData-class Man page
InData.validity Source code
LS041 Man page
MQR Source code
MQRDS Source code
OTquantileWeights Source code
Params-class Man page
R Source code
Rb Source code
Rcheck Source code
Res.summary Source code
TTquantileWeights Source code
[,CNAnorm-method Man page
addDNACopy Man page Source code
addDNACopy,CNAnorm-method Man page
addDNACopy-methods Man page
addSmooth Man page Source code
addSmooth,CNAnorm-method Man page
addSmooth-methods Man page
arms Man page Source code
arms,CNAnorm-method Man page
arms-methods Man page
bandseg Source code
brute.seg Source code
brute.solve Source code
bsolve00 Source code
buildWarn Source code
calcWeight Source code
checkMethod Source code
chrs Man page
chrs,CNAnorm-method Man page
chrs-methods Man page
chrs<- Man page
chrs<-,CNAnorm-method Man page
chrs<--methods Man page
cumGenPosition Source code
dataFrame2object Man page Source code
discreteNorm Man page Source code
discreteNorm,CNAnorm-method Man page
discreteNorm-methods Man page
exportTable Man page Source code
exportTable,CNAnorm-method Man page
exportTable-methods Man page
findOutliers Source code
gPar Man page
gaussianWeights Source code
gcNorm Man page Source code
gcNorm,CNAnorm-method Man page
gcNorm-methods Man page
gcNormalize Source code
get.initial.values Source code
get.optimal.k Source code
get.optimal.k.reg Source code
getMQR Source code
getWeight Source code
getWeightByChr Source code
global.norm Source code
guessPeaksAndPloidy Source code
hg19_hs_ideogr Man page
inData.summary Source code
justRatio Source code
length,CNAnorm-method Man page Man page
length,DerivData-method Man page
length,InData-method Man page
makeDataFrameFromSlots Source code
makeDefaultGraphParamteres Source code
makeNumericLabels Source code
makeTextLabels Source code
manualValidation Source code
mapPeaks Source code
medianWinSize Source code
myDensity Source code
myPeaks Source code
pdetect Source code
pdetect.iter Source code
peakPloidy Man page Source code
peakPloidy,CNAnorm-method Man page
peakPloidy-methods Man page
plotGenome Man page Source code
plotGenome,CNAnorm-method Man page
plotGenome-methods Man page
plotPeaks Man page Source code
plotPeaks,CNAnorm-method Man page
plotPeaks-methods Man page
plotPeaksMixture Source code
plotPeaks_old Source code
poissonWeights Source code
pos Man page Source code
pos,CNAnorm-method Man page
pos-methods Man page
pos2chr Source code
pos<- Man page
pos<-,CNAnorm-method Man page
pos<--methods Man page
possibleBinNumbers Source code
ratio Man page
ratio,CNAnorm-method Man page
ratio-methods Man page
ratio.n Man page
ratio.n,CNAnorm-method Man page
ratio.n-methods Man page
ratio.s Man page
ratio.s,CNAnorm-method Man page
ratio.s-methods Man page
ratio.s.n Man page
ratio.s.n,CNAnorm-method Man page
ratio.s.n-methods Man page
ratio2use Source code
rseg Source code
sameLength Source code
segMean Man page
segMean,CNAnorm-method Man page
segMean-methods Man page
segMean.n Man page
segMean.n,CNAnorm-method Man page
segMean.n-methods Man page
selectGoodGuess Source code
showCNAnorm Source code
smooth.it Source code
smoothSignal Source code
specialDensity Source code
srsmooth Source code
startStop Source code
subSet Source code
sugg.peaks Man page
sugg.peaks,CNAnorm-method Man page
sugg.peaks-methods Man page
sugg.ploidy Man page
sugg.ploidy,CNAnorm-method Man page
sugg.ploidy-methods Man page
suggest.k Source code
userOrDefault Source code
valid.peaks Man page
valid.peaks,CNAnorm-method Man page
valid.peaks-methods Man page
valid.ploidy Man page
valid.ploidy,CNAnorm-method Man page
valid.ploidy-methods Man page
validateParams Source code
validation Man page Source code
validation,CNAnorm-method Man page
validation-methods Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/CNAnorm-accessors.R
R/CNAnorm-methods.R
R/Data-methods.R
R/bandsegment.R
R/dataFrame2object.R
R/initialize-methods.R
R/length-methods.R
R/makeDefaultGraphParamteres.R
R/mixtureModel.R
R/normalize.R
R/smoothseg.R
R/summary-methods.R
R/workflowWrapper.R
build
build/vignette.rds
data
data/CN.RData
data/LS041.RData
data/gPar.RData
data/hg19_hs_ideogr.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/CNAnorm.R
inst/doc/CNAnorm.Snw
inst/doc/CNAnorm.pdf
man
man/CN.Rd
man/CNAnorm-class.Rd
man/DerivData-class.Rd
man/InData-class.Rd
man/LS041.Rd
man/Params-class.Rd
man/addDNACopy-methods.Rd
man/addSmooth-methods.Rd
man/chrsAndpos-methods.Rd
man/data-hg19_hs_ideogr.Rd
man/dataFrame2object.Rd
man/discreteNorm-methods.Rd
man/exportTable-method.Rd
man/gPar.Rd
man/gcNorm-methods.Rd
man/peakPloidy.Rd
man/plotGenome-methods.Rd
man/plotPeaks-methods.Rd
man/ratio-methods.Rd
man/suggValid-methods.Rd
man/validation-methods.Rd
man/workflowWrapper.Rd
src
src/daxpy.f
src/ddot.f
src/dgbfa.f
src/dgbsl.f
src/dscal.f
src/dsmooth.f
src/idamax.f
vignettes
vignettes/CNAnorm.Snw
vignettes/ref.bib
CNAnorm documentation built on May 20, 2017, 9:47 p.m.