\HeaderA{amplicon.plot}{Create an amplicon plot}{amplicon.plot}
\keyword{hplot}{amplicon.plot}
\begin{Description}\relax
Given a two-sample test statistic and an ExpressionSet this function plots
regions of the genome that are either highly expressed (in red) or
have low expression (blue) differentially in the two groups.
\end{Description}
\begin{Usage}
\begin{verbatim}
amplicon.plot(ESET, FUN, genome)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ESET}] an object of class \code{ExpressionSet}
\item[\code{FUN}] A two sample test function suitable for \code{\LinkA{esApply}{esApply}}. 
\item[\code{genome}] A character string of the base name for the annotation. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
In some genetic studies we are interested in finding regions of the
genome where there are a set of highly expressed genes in some
subgroup of the population. This set of highly (or lowly) expressed
genes is often of great interest. For example in breast cancer the
HER--2 gene is on an amplicon. In some patients approximately 5 genes
located near HER--2 are all amplified.

These plot should help in the search for such regions.
\end{Details}
\begin{Value}
No value is returned. This function is executed purely for side
effect.
\end{Value}
\begin{Author}\relax
Robert Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{esApply}{esApply}}, \code{\LinkA{make.chromOrd}{make.chromOrd}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  ##none yet; takes too long
\end{ExampleCode}
\end{Examples}

