\HeaderA{sort}{Sorting for normalized arrayCGH objects}{sort}
\methaliasA{sort.arrayCGH}{sort}{sort.arrayCGH}
\keyword{utilities}{sort}
\begin{Description}\relax
Sorts clone-level information of a normalized arrayCGH object.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## S3 method for class 'arrayCGH':
  sort(x, decreasing = FALSE, position.var="Position",
    chromosome.var="Chromosome", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object of type \code{arrayCGH}.
\item[\code{decreasing}] (for compatibility with \code{sort} class) currently unused.
\item[\code{position.var}] name of position variable.
\item[\code{chromosome.var}] name of chromosome variable.
\item[\code{...}] further arguments to be passed to \code{sort}.
\end{ldescription}
\end{Arguments}
\begin{Note}\relax
People interested in tools for array-CGH analysis can
visit our web-page: \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Pierre Neuvial, \email{manor@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{norm.arrayCGH}{norm.arrayCGH}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)

## sort a normalized array by clone position
gradient.norm <- sort(gradient.norm)

report.plot(gradient.norm, main="Genomic profile after normalization")
\end{ExampleCode}
\end{Examples}

