##' DefineCNVClass: Define the CNV class.
##'
##' Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.
##' @title DefineCNVClass
##' @param tmp2: Unknown
##' @return CNV class.
##' @author Marcelo Bertalan, Louise K. Hoeffding.
##' @source \url{http://biopsych.dk/iPsychCNV}
##' @export
##' @examples Uknown
##'
DefineCNVClass <- function(tmp2)
{
Type <- apply(tmp2, 1, function(X)
{
Class <- 2
if(X["LogRRatio"] %in% X["MyBAF"] & !X["LogRRatio"] %in% "2" )
{
#Class <- GetCNVClass(X["LogRRatio"])
Class <- X["LogRRatio"]
}
else if(X["LogRRatio"] %in% X["PamBAF"] & !X["LogRRatio"] %in% "2" ) # Just to avoid 2 Undefined being good.
{
#Class <- GetCNVClass(X["LogRRatio"])
Class <- X["LogRRatio"]
}
else
{
if(X["LogRRatio"] == 1 & X["MyBAF"] == 0)
{
Class <- 0
}
else if(X["LogRRatio"] == 3 & X["MyBAF"] == 4)
{
Class <- 4
}
else if(X["LogRRatio"] == 3 & X["MyBAF"] == 1) # Duplication with LOH.
{
Class <- 2 # removing 5, not working well.
}
}
return(Class)
})
return(Type)
}
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