\inputencoding{latin1}
\HeaderA{arrayTrend}{Spatial trend of microarray spots statistic}{arrayTrend}
\methaliasA{arrayTrend.arrayCGH}{arrayTrend}{arrayTrend.arrayCGH}
\methaliasA{arrayTrend.default}{arrayTrend}{arrayTrend.default}
\keyword{smooth}{arrayTrend}
\keyword{loess}{arrayTrend}
\keyword{spatial}{arrayTrend}
\begin{Description}\relax
The function \code{arrayTrend} computes the spatial trend.
\end{Description}
\begin{Usage}
\begin{verbatim}
## Default S3 method:
arrayTrend(Statistic, Col, Row, ...)
## S3 method for class 'arrayCGH':
arrayTrend(arrayCGH, variable, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{Statistic}] Statistic to be smoothed.
\item[\code{Col}] Vector of columns coordinates.
\item[\code{Row}] Vector of rows coordinates.
\item[\code{arrayCGH}] Object of class \code{\LinkA{arrayCGH}{arrayCGH}}.
\item[\code{variable}] Variable to be smooth.
\item[\code{...}] Parameters to be passed to \code{\LinkA{loess}{loess}} function.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Spatial trend of microarray spots statistic.
\end{Details}
\begin{Value}
Either a data frame with elements :
\begin{ldescription}
\item[\code{Trend}] Trend fitted by \code{\LinkA{loess}{loess}} function.
\item[\code{Col}] Vector of columns coordinates.
\item[\code{Row}] Vector of rows coordinates.
\end{ldescription}

or the element \code{Trend} is added to the data.frame \code{arrayValues}
of the \code{arrayCGH} object.
\end{Value}
\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
Philippe Hupé, \email{Philippe.Hupe@curie.fr}.
\end{Author}
\begin{References}\relax
P. Neuvial, P. Hupé, I. Brito, S. Liva, E. Manié, C. Brennetot,
A. Aurias, F. Radvanyi, and E. Barillot. \emph{Spatial normalization
of array-CGH data}. BMC Bioinformatics, 7(1):264. May 2006.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{loess}{loess}}, \code{\LinkA{loess.control}{loess.control}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)  ## arrays with local spatial effects

edgeTrend <- arrayTrend(edge, "LogRatio", span=0.03, degree=1,
iterations=3, family="symmetric") 
arrayPlot(edgeTrend, "Trend", main="Spatial trend of array CGH", bar="v") 
\end{ExampleCode}
\end{Examples}

