\HeaderA{flags}{Examples of flag objects to apply to CGH arrays}{flags}
\aliasA{amplicon.flag}{flags}{amplicon.flag}
\aliasA{chromosome.flag}{flags}{chromosome.flag}
\aliasA{control.flag}{flags}{control.flag}
\aliasA{dapi.snr.flag}{flags}{dapi.snr.flag}
\aliasA{global.spatial.flag}{flags}{global.spatial.flag}
\aliasA{intensity.flag}{flags}{intensity.flag}
\aliasA{local.spatial.flag}{flags}{local.spatial.flag}
\aliasA{position.flag}{flags}{position.flag}
\aliasA{ref.snr.flag}{flags}{ref.snr.flag}
\aliasA{rep.flag}{flags}{rep.flag}
\aliasA{replicate.flag}{flags}{replicate.flag}
\aliasA{SNR.flag}{flags}{SNR.flag}
\aliasA{spatial.flag}{flags}{spatial.flag}
\aliasA{spot.flag}{flags}{spot.flag}
\aliasA{unique.flag}{flags}{unique.flag}
\aliasA{val.mark.flag}{flags}{val.mark.flag}
\keyword{datasets}{flags}
\begin{Description}\relax
This data set provides \code{\LinkA{flag}{flag}} objects that can be applied to \code{arrayCGH}
objects in order to normalize them.
\end{Description}
\begin{Usage}
\begin{verbatim}data(flags)\end{verbatim}
\end{Usage}
\begin{Format}\relax
These \code{flag} objects typically take part to a normalization process:
\Tabular{lll}{
& \code{amplicon.flag} & flags spots with high log-ratios (temp flag) \\
& \code{chromosome.flag} & flags spots located on sexual
chromosomes (named "X" and "Y") \\
& \code{control.flag} & flag control spots \\
& \code{global.spatial.flag} & corrects arrayCGH from global
spatial trend on the array\\
& \code{local.spatial.flag} & flags spots belonging to local spatial bias zones on the array \\
& \code{num.chromosome.flag} & flags spots located on sexual
chromosomes (named 23 and 24)\\
& \code{position.flag} & flag spots with no available genome
position \\
& \code{replicate.flag} & flag spots with poor within-clone-replicate consitency \\
& \code{ref.snr.flag} & flags spots with low signal to noise
ratio for reference \\
& \code{dapi.snr.flag} & flags spots with low signal to noise
ratio for DAPI \\
& \code{SNR.flag} & flags spots with low signal to noise ratio \\
& \code{spot.corr.flag} & flags spots with low correlation
coefficient after image analysis \\
& \code{spot.flag} & flags spots excluded by the image
analysis software \\
& \code{unique.flag} & exclude last non-flagged spot of a clone \\ 
& \code{val.mark.flag} & flags spots corresponding to bad quality clones \\
& \code{intensity.flag} & corrects for an intensity effect
(using loess regression) \\
}
\end{Format}
\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{Source}\relax
Institut Curie, \email{manor@curie.fr}.
\end{Source}
\begin{SeeAlso}\relax
\code{\LinkA{spatial}{spatial}}, \code{\LinkA{norm.arrayCGH}{norm.arrayCGH}},
\code{\LinkA{flag}{flag}}, \code{\LinkA{flag.summary}{flag.summary}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(flags)

### complete normalization of an arrayCGH object (with spatial gradient):
## Initialize flag$args

flag.list1 <- list(local.spatial=local.spatial.flag,
  global.spatial=global.spatial.flag, spot=spot.flag, SNR=SNR.flag,
  val.mark=val.mark.flag, unique=unique.flag,
  amplicon=amplicon.flag, chromosome=chromosome.flag,
  replicate=replicate.flag)

data(spatial)
## Not run: 
gradient.norm <- norm.arrayCGH(gradient, flag.list=flag.list1,
var="LogRatio", FUN=median, na.rm=TRUE)
## End(Not run)
print(gradient.norm$flags) ## spot-level flag summary (computed by flag.summary)

### complete normalization of an arrayCGH object (with local spatial bias):
## Initialize flag$args

flag.list2 <- 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.list2$spatial$args <- alist(var="ScaledLogRatio", by.var=NULL,
nk=5, prop=0.25, thr=0.15, beta=1, family="symmetric") 
flag.list2$spot$args <- alist(var="SpotFlag")
flag.list2$spot$char <- "O"
flag.list2$spot$label <- "Image analysis"

## Not run: 
edge.norm <- norm.arrayCGH(edge, flag.list=flag.list2,
var="LogRatio", FUN=median, na.rm=TRUE)
## End(Not run) 
print(edge.norm$flags) ## spot-level flag summary (computed by flag.summary)
\end{ExampleCode}
\end{Examples}

