CNAnormWorkflow {CNAnorm} | R Documentation

## Wrapper to `"CNAnorm"` workflow

### Description

This function is a wrapper to use for a fully automated CNAnorm workflow where interactivity is not required. It contains MOST possible paramenters. Defaults are set to to run a standard and conservative workflow.

### Usage

    CNAnormWorkflow(dataFrame, gc.do=FALSE, gc.exclude=character(0),
        gc.maxNumPoints=10000, smooth.do=TRUE, smooth.lambda=7,
        smooth.other=list(), peak.method='closest', peak.exclude=character(0),
        peak.ploidyToTest=12, peak.sd=5, peak.dThresh=0.01, peak.n=2048,
        peak.adjust=.9, peak.force.smooth=TRUE, peak.reg=FALSE, peak.ds=1.5,
        peak.zero.count=FALSE, peak.other=list(), DNAcopy.do=TRUE,
        DNAcopy.independent.arms=FALSE, DNAcopy.ideograms=NULL,
        DNAcopy.smooth=list(), DNAcopy.segment=list(), DNAcopy.weight=character(),
        dNorm.normBy=NULL)

### Arguments

All arguments are explained in the relative functions

`dataFrame` | A data frame with columns Chr, Pos, Test, Norm and optional GC. See dataFrame2object
`gc.do` | Specify if GC correction need to be done. See gcNorm
`gc.exclude` | See gcNorm
`gc.maxNumPoints` | See gcNorm
`smooth.do` | Specify if smoothing need to be done. See addSmooth
`smooth.lambda` | See addSmooth
`smooth.other` | A list of other parameters to pass to the smoothing function. See addSmooth
`peak.method` | See peakPloidy
`peak.exclude` | See peakPloidy
`peak.ploidyToTest` | See peakPloidy
`peak.sd` | See peakPloidy
`peak.dThresh` | See peakPloidy
`peak.n` | See peakPloidy
`peak.adjust` | See peakPloidy
`peak.force.smooth` | See peakPloidy
`peak.reg` | See peakPloidy
`peak.ds` | See peakPloidy
`peak.zero.count` | See peakPloidy
`peak.other` | A list of other parameters to be passed to funtions for peak detection See peakPloidy
`DNAcopy.do` | Specify if segmentation with DNAcopy need to be done. See addDNACopy
`DNAcopy.independent.arms` | See addDNACopy
`DNAcopy.ideograms` | See addDNACopy
`DNAcopy.smooth` | See addDNACopy
`DNAcopy.segment` | See addDNACopy
`DNAcopy.weight` | See addDNACopy
`dNorm.normBy` | See discreteNorm

### Value

An object of Class `"CNAnorm"`

### Author(s)

Stefano Berri <s.berri@leeds.ac.uk>

### See Also

`dataFrame2object`, `gcNorm`, `addSmooth`, `peakPloidy`, `addDNACopy`, `discreteNorm`

### Examples

    data(LS041)
    CN <- CNAnormWorkflow(LS041)

[Package CNAnorm version 1.36.0 Index]