CNAnorm (version 1.18.0)

CNAnormWorkflow: 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

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"

See Also

dataFrame2object, gcNorm, addSmooth, peakPloidy, addDNACopy, discreteNorm

Examples

data(LS041)
CN <- CNAnormWorkflow(LS041)