\HeaderA{compareSemmentations}{Function for comparing segmentation methods to a known truth}{compareSemmentations}
\aliasA{compareBreakPoints}{compareSemmentations}{compareBreakPoints}
\aliasA{compareSegmentations}{compareSemmentations}{compareSegmentations}
\keyword{manip}{compareSemmentations}
\begin{Description}\relax
This function takes a SegList and compares the breakpoints indicated
in other SegLists with this original one.
\end{Description}
\begin{Usage}
\begin{verbatim}
compareSegmentations(TrueSeg,offset = 0,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{TrueSeg}] An object of class
\code{\LinkA{SegList}{SegList}} which is scored against.
Normally the output from \code{\LinkA{simulateData}{simulateData}}.
\item[\code{offset}] Integer value between 0 and 2 specifying how close (in
number of clones) to a true breakpoint the segmentation method must be before it is scored.
\item[\code{...}] One or more objects of class
\code{\LinkA{SegList}{SegList}}.  These are compared to TrueSeg.
\end{ldescription}
\end{Arguments}
\begin{Value}
The method returns a list containing two 
matrices.  The first of these, \$TPR, contains the true positive rate, 
whilst the second, \$FDR, holds the false discovery rate.  Both of these
matrices are arranged such that a row represents a segmentation method and 
each column is an array.
\end{Value}
\begin{Author}\relax
John Marioni and Mike Smith
\end{Author}

