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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNAnorm")
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
Version1.20.0
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,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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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