R/RunSingleMock.R

In mbertalan/iPsychCNV: iPsychCNV

##' RunSingleMock: Run a single mock sample.   
##'
##' Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.
##' @title RunSingleMock
##' @param Noise: Unknown, default = 0.
##' @param CNVMean: Unknown, default = 0.4.
##' @param Name: Unknown, default =Unknown.
##' @param Method: The CNV predicting algorithm, default = PennCNV.
##' @return Classification for Log R Ratio (LRR).
##' @author Marcelo Bertalan, Louise K. Hoeffding.
##' @source \url{http://biopsych.dk/iPsychCNV}
##' @export
##' @examples Unknown.
##'

RunSingleMock <- function(Noise=0, CNVMean=0.4, Name="Test", Method="PennCNV")
{
	tmp <- MakeOneMockSample(Noise=Noise, CNVMean=CNVMean)
	if(Method %in% "PennCNV")
	{
		PredictedCNV <- RunPennCNV(PathRawData=".", Pattern="MockSample_1.tab$", Cores=1, Skip=0, Normalization=FALSE, PFB="")
	}
	else if(Method %in% "iPsychCNV")
	{
		PredictedCNV <- iPsychCNV(PathRawData=".", MINNumSNPs=28, Cores=1, Pattern="MockSample_1.tab$", MinLength=10, Skip=0, LCR=FALSE)
	}
	else if(Method %in% "Gada")
	{
		PredictedCNV <- RunGada(tmp)
	}	

	Name <- paste(Name, "_Noise", Noise, "_CNVmean", CNVMean, ".png", sep="", collapse="")
	PlotLRRAndCNVs(PredictedCNV, tmp, CNVMean, Name=Name, Roi=RoiSingleMock)
}