\HeaderA{flag.arrayCGH}{Apply a flag to an arrayCGH}{flag.arrayCGH}
\aliasA{flag}{flag.arrayCGH}{flag}
\keyword{misc}{flag.arrayCGH}
\begin{Description}\relax
Function \code{flag\$FUN} is applied to a \code{flag} object for
normalization
\end{Description}
\begin{Usage}
\begin{verbatim}flag.arrayCGH(flag, arrayCGH)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{flag}] an object of type 'flag'
\item[\code{arrayCGH}] an object of type \code{\LinkA{arrayCGH}{arrayCGH}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Optional arguments in \code{flag\$args} are passed to
\code{flag\$FUN}
\end{Details}
\begin{Value}
An object of class \code{arrayCGH}, which corresponds to the return
value of \code{flag\$FUN} if \code{flag\$char} is null, and to the
input \code{arrayCGH} object with spots given by \code{flag\$FUN}
flagged with \code{flag\$char}
\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{to.flag}{to.flag}}, \code{\LinkA{norm.arrayCGH}{norm.arrayCGH}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)
data(flags)

gradient$arrayValues$LogRatioNorm <- gradient$arrayValues$LogRatio
## flag spots with no available position on the genome
gradient <- flag.arrayCGH(position.flag, gradient)

## flag spots corresponding to low poor quality clones
gradient <- flag.arrayCGH(val.mark.flag, gradient)

## flag spots excluded by Genepix pro
gradient <- flag.arrayCGH(spot.flag, gradient)

## flag local spatial bias zones
## Not run: gradient <- flag.arrayCGH(local.spatial.flag, gradient)

## correct global spatial bias
gradient <- flag.arrayCGH(global.spatial.flag, gradient)

## flag spots with low signal to noise
gradient <- flag.arrayCGH(SNR.flag, gradient)

## flag spots with extremely high log-ratios
gradient <- flag.arrayCGH(amplicon.flag, gradient)

## flag spots with poor within replicate consistency
gradient <- flag.arrayCGH(replicate.flag, gradient)

## flag spots corresponding to clones for which all other spot
## replicates have already been flagged  
gradient <- flag.arrayCGH(unique.flag, gradient)

summary.factor(gradient$arrayValues$Flag)
\end{ExampleCode}
\end{Examples}

