CNAnormWorkflow {CNAnorm} | R Documentation |
"CNAnorm"
workflowThis 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 |
An object of Class "CNAnorm"
Stefano Berri <s.berri@leeds.ac.uk>
dataFrame2object
, gcNorm
, addSmooth
,
peakPloidy
, addDNACopy
, discreteNorm
data(LS041) CN <- CNAnormWorkflow(LS041)