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CNAnorm (version 1.18.0)

A normalization method for Copy Number Aberration in cancer samples

Description

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.

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Version

Version

1.18.0

License

GPL-2

Homepage

http://www.r-project.org

Maintainer

Stefano Berri

Last Published

February 15th, 2017

Functions in CNAnorm (1.18.0)

Mapped reads in tumor and matched blood for patient LS041

Methods for Function plotGenome in Package `CNAnorm'

chromosomesPosition

Accessors methods for Function ratio in Package `CNAnorm'

Class "InData" ~~~

CNAnormWorkflow

Wrapper to "CNAnorm" workflow

Methods for Function exportTable in Package `CNAnorm'

Methods for Function addSmooth in Package `CNAnorm'

retrieve peaks and ploidy

Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm'

DerivData-class

Class "DerivData"

Methods for Function gcNorm in Package `CNAnorm'

An object with the default graphical parameters

An object with the ideogram information for homo sapiens - hg19

Methods for Function addDNACopy in Package `CNAnorm'

Methods for Function addSmooth in Package `CNAnorm'

Methods for Function ratio in Package `CNAnorm'

Methods for Function plotPeaks in Package `CNAnorm'

A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.

Methods for Function peakPloidy in Package `CNAnorm'

Methods for Function addSmooth in Package `CNAnorm'

Class "CNAnorm"

dataFrame2object

Convert a data frame into an object of Class "CNAnorm"