# A normalization method for Copy Number Aberration in cancer samples

## Documentation for package ‘CNAnorm’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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