\HeaderA{idPoints}{Identify points in sample point matrix plot}{idPoints}
\keyword{iplot}{idPoints}
\begin{Description}\relax
Identify points in sample point matrix plot
\end{Description}
\begin{Usage}
\begin{verbatim}
idPoints(spm, mode='pos', dev=2, chromosomes=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{spm}] The sample point matrix object of which points are to be identified 
\item[\code{mode}] Determines which points will be identified: mode='pos' will identify points in gained regions, mode='neg' will identify points in lost regions 
\item[\code{dev}] The device on which the sample point matrix was plotted
\item[\code{chromosomes}] 
\end{ldescription}
 { If not all chromosomes contained in the sample point matrix were plotted (using the 'chromosomes' argument in the 'plot' command), the same chromosomes must be entered here as an argument}
\end{Arguments}
\begin{Details}\relax
Using the mouse pointer points in a sample point matrix plot can be identified by left-clicking on the to-be-identified points. Right-clicking exits the selection and returns the selected points.
\end{Details}
\begin{Value}
Returns a data.frame listing the the position and the KC score for each identified point.
\begin{ldescription}
\item[\code{KCscore}] KCscore of the identified point
\item[\code{chromosome}] Chromosome on which the identified point is located
\item[\code{chromPosition}] Position on the chromosome of the identified point
\item[\code{colin}] Co-linear location of the identified point (given the selected chromosomes)
\end{ldescription}
\end{Value}
\begin{Author}\relax
Jorma de Ronde
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{plot}{plot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(hsSampleData)
data(hsMirrorLocs)

#spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

#plot(spm1mb, type=1)
#idPoints(spm1mb)

#x11()
#plot(spm1mb, chromosomes=c(1,2,5))
#idPoints(spm1mb, mode='neg', dev=3, chromosomes=c(1,2,5))
\end{ExampleCode}
\end{Examples}

