##' DefineCNVType: Determine true CNVs calls.
##'
##' Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.
##' @title DefineCNVType
##' @param tmp2: Unknown.
##' @return CNV type.
##' @author Marcelo Bertalan, Louise K. Hoeffding
##' @source \url{http://biopsych.dk/iPsychCNV}
##' @export
##' @examples Unknown
##'
DefineCNVType <- function(tmp2)
{
Type <- apply(tmp2, 1, function(X)
{
if(X["LogRRatio"] %in% X["MyBAF"] & !X["LogRRatio"] %in% "Undefined" )
{
return("Good")
}
else if(X["LogRRatio"] %in% X["MyBAF"] )
{
if(!X["LogRRatio"] %in% "Undefined") # Just to avoid 2 Undefined being good.
{
return("Good")
}
else
{
return("Bad")
}
}
else
{
return("Bad")
}
})
return(Type)
}
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