\HeaderA{ROC}{Creates an object of class "ROC" which can be plotted as a ROC curve}{ROC}
\aliasA{lines.ROC}{ROC}{lines.ROC}
\aliasA{plot.ROC}{ROC}{plot.ROC}
\keyword{univar}{ROC}
\begin{Description}\relax
The function \code{ROC} construct an object of S3 class \code{ROC},
which represents a receiver-operator-characteristic curve,
from the data of the annotated positive and negative controls in a
scored cellHTS object.
\end{Description}
\begin{Usage}
\begin{verbatim}
ROC(x, positives="pos", negatives = "neg")
## S3 method for class 'ROC':
plot(x, col="darkblue", type="l", ...)
## S3 method for class 'ROC':
lines(x, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a cellHTS object that has already been scored (see details).
\item[\code{positives}] a character string corresponding to the name used to
annotate the positive controls in the cellHTS object.
\item[\code{negatives}] a character string corresponding to the name used to
annotate the negative controls in the cellHTS object.
\item[\code{col}] the graphical parameter for color; see \code{\LinkA{par}{par}} for details.
\item[\code{type}] the graphical parameter giving the type of plot desired; see \code{\LinkA{par}{par}} for details.
\item[\code{...}] other graphical parameters as in \code{\LinkA{par}{par}} may be also passed as arguments.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \code{cellHTS} object \code{x} must contain a slot called \code{score},
and selection proceeds from large to small values of this score.
Furthermore, \code{x} is expected to contain positive and negative
controls annotated in the slot \code{wellAnno} with the values of
the arguments \code{positives} and \code{negatives}, respectively.
\end{Details}
\begin{Value}
An S3 object of class \code{ROC}. There are methods
\code{plot.ROC} and \code{lines.ROC}.
\end{Value}
\begin{Author}\relax
W. Huber \email{huber@ebi.ac.uk}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
 datadir = system.file("KcViabSmall", package = "cellHTS")
 x = readPlateData("Platelist.txt", "KcViabilitySmall", path=datadir)
 confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
 logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
 descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
 x = configure(x, confFile, logFile, descripFile)
 x = normalizePlateMedian(x, zscore="-")
 x = summarizeReplicates(x)
 y = ROC(x)
 plot(y)
 lines(y)
\end{ExampleCode}
\end{Examples}

