\HeaderA{flag.summary}{Summarize information about flags after array normalization}{flag.summary}
\methaliasA{flag.summary.arrayCGH}{flag.summary}{flag.summary.arrayCGH}
\methaliasA{flag.summary.default}{flag.summary}{flag.summary.default}
\keyword{misc}{flag.summary}
\begin{Description}\relax
Compute spot-level information (number of flagged spots, normalization
parameters), and display it in a convenient way
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'arrayCGH':
flag.summary(arrayCGH, flag.list, flag.var="Flag", nflab="not flagged", ...)
## Default S3 method:
flag.summary(spot.flags, flag.list, nflab="not flagged", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayCGH}] an object of type arrayCGH, \emph{after normalization}
by MANOR
\item[\code{flag.list}] a list of flags with \code{flag\$char} corresponding
to the values of \code{spot.flags}
\item[\code{flag.var}] the name of a variable of arrayCGH\$arrayValues
containing information about flags (defaults to \code{Flag})
\item[\code{var}] the name of a variable of arrayCGH\$cloneValues containing
signal values (defaults to \code{LogRatio})
\item[\code{spot.flags}] a character vector containing information about
flags
\item[\code{nflab}] a character vector providing a legend for "not flagged" spots
\item[\code{...}] 
\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 data.frame with 4 columns:
\begin{ldescription}
\item[\code{name}] flag character
\item[\code{label}] flag label
\item[\code{arg}] first numeric argument of \code{flag\$FUN}
\item[\code{count}] number of flagged spots
\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{html.report}{html.report}}, \code{\LinkA{flag}{flag}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)
data(flags)
flag.list <- list(spatial=local.spatial.flag, spot=spot.corr.flag,
ref.snr=ref.snr.flag, dapi.snr=dapi.snr.flag, rep=rep.flag,
unique=unique.flag) 
flag.list$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
flag.list$spot$args <- alist(var="SpotFlag")
flag.list$spot$char <- "O"
flag.list$spot$label <- "Image analysis"

## normalize arrayCGH
## Not run: 
edge.norm <- norm(edge, flag.list=flag.list,
var="LogRatio", FUN=median, na.rm=TRUE)
## End(Not run) 
fs <- flag.summary(edge.norm, flag.list=flag.list, flag.var="Flag")

print("Flag and normalization parameters summary")
print(fs)
\end{ExampleCode}
\end{Examples}

