\HeaderA{qscore.summary}{Compute quality scores for a given arrayCGH object}{qscore.summary}
\methaliasA{qscore.summary.arrayCGH}{qscore.summary}{qscore.summary.arrayCGH}
\keyword{misc}{qscore.summary}
\begin{Description}\relax
Compute useful quality scores for the \code{arrayCGH} and display them
in a convenient way
\end{Description}
\begin{Usage}
\begin{verbatim}qscore.summary.arrayCGH(arrayCGH, qscore.list)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayCGH}] an object of type \code{arrayCGH}
\item[\code{qscore.list}] a list of objects of type \code{\LinkA{qscore}{qscore}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is used by the function \code{html.report} for
the generation of an HMTL report of the normalization step.
It can also be used by itself.
\end{Details}
\begin{Value}
A data.frame with 3 columns:
\begin{ldescription}
\item[\code{name}] qscore name
\item[\code{label}] qscore label
\item[\code{qscore}] quality qscore
\end{ldescription}
\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
Pierre Neuvial, \email{manor@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{qscore}{qscore}}, \code{\LinkA{qscore.summary}{qscore.summary}}, \code{\LinkA{html.report}{html.report}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(qscores)
data(spatial)

## define a list of qscores
qscore.list <- list(clone=clone.qscore, pct.clone=pct.clone.qscore,
pct.spot=pct.spot.qscore, pct.replicate=pct.replicate.qscore,
smoothness=smoothness.qscore, dyn.x=dyn.x.qscore, dyn.y=dyn.y.qscore,
var.replicate=var.replicate.qscore)

## compute quality scores for a couple of normalized arrays
gradient.norm$quality <- qscore.summary.arrayCGH(gradient.norm,
qscore.list)
print(gradient.norm$quality[, 2:3])

qscore.list$dyn.x$args$test <- 23
qscore.list$dyn.y$args$test <- 24
edge.norm$quality <- qscore.summary.arrayCGH(edge.norm, qscore.list)
print(edge.norm$quality[, 2:3])
\end{ExampleCode}
\end{Examples}

