workflowWrapper: Wrapper to '"CNAnorm"' workflow
In CNAnorm: A normalization method for Copy Number Aberration in cancer samples

Description Usage Arguments Value Author(s) See Also Examples

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.

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)

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