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.
|Author||Stefano Berri <email@example.com>, Henry M. Wood <H.M.Wood@leeds.ac.uk>, Arief Gusnanto <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Stefano Berri <email@example.com>|
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