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.

AuthorStefano Berri <sberri@illumina.com>, Henry M. Wood <H.M.Wood@leeds.ac.uk>, Arief Gusnanto <a.gusnanto@leeds.ac.uk>
Date of publicationNone
MaintainerStefano Berri <sberri@illumina.com>
LicenseGPL-2
Version1.20.0
http://www.r-project.org,

View on Bioconductor

Functions

addDNACopy Man page
addDNACopy,CNAnorm-method Man page
addDNACopy-methods Man page
addSmooth Man page
addSmooth,CNAnorm-method Man page
addSmooth-methods Man page
arms Man page
arms,CNAnorm-method Man page
arms-methods Man page
chrs Man page
chrs<- Man page
chrs<-,CNAnorm-method Man page
chrs,CNAnorm-method Man page
chrs<--methods Man page
chrs-methods Man page
CN Man page
CNAnorm Man page
CNAnorm-class Man page
[,CNAnorm-method Man page
CNAnormWorkflow Man page
dataFrame2object Man page
DerivData-class Man page
discreteNorm Man page
discreteNorm,CNAnorm-method Man page
discreteNorm-methods Man page
exportTable Man page
exportTable,CNAnorm-method Man page
exportTable-methods Man page
gcNorm Man page
gcNorm,CNAnorm-method Man page
gcNorm-methods Man page
gPar Man page
hg19_hs_ideogr Man page
InData-class Man page
length,CNAnorm-method Man page
length,CNAnorm-method Man page
length,DerivData-method Man page
length,InData-method Man page
LS041 Man page
Params-class Man page
peakPloidy Man page
peakPloidy,CNAnorm-method Man page
peakPloidy-methods Man page
plotGenome Man page
plotGenome,CNAnorm-method Man page
plotGenome-methods Man page
plotPeaks Man page
plotPeaks,CNAnorm-method Man page
plotPeaks-methods Man page
pos Man page
pos<- Man page
pos<-,CNAnorm-method Man page
pos,CNAnorm-method Man page
pos<--methods Man page
pos-methods Man page
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
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
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
validation Man page
validation,CNAnorm-method Man page
validation-methods Man page
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

Files

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

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