\HeaderA{html.report}{Generate an HTML report of array normalization}{html.report}
\methaliasA{html.report.arrayCGH}{html.report}{html.report.arrayCGH}
\methaliasA{html.report.default}{html.report}{html.report.default}
\begin{Description}\relax
Create an HTML file with various illustrations of array normalization,
including plots before and after normalization, and statistics about
flagged spots and clones
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## S3 method for class 'arrayCGH':
  html.report(array.norm, array.nonorm=NULL, dir.out=".",
array.name=NULL, x="PosOrder", y=c("LogRatioNorm", "LogRatio"), chrLim=NULL,
ylim=NULL, zlim=NULL, clim=NULL, intensity=NULL, light=FALSE, file.name="report",
width=10, height=5, ...) 
  ## Default S3 method:
  html.report(spot.data, clone.data=NULL, flag.data=NULL, quality.data=NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{array.norm}] an object of type \code{arrayCGH} after normalization step
\item[\code{array.nonorm}] an optional object of type arrayCGH after a
normalization step with no flags
\item[\code{spot.data}] a data.frame containing spot-level informations
(e.g. \code{arrayCGH\$arrayValues})
\item[\code{clone.data}] a data.frame containing clone-level informations
(e.g. \code{arrayCGH\$cloneValues})
\item[\code{flag.data}] a data.frame containing information about flags, with
fields \code{char}, \code{label}, \code{arg}, \code{count} as
generated by function \code{\LinkA{flag.summary}{flag.summary}}
\item[\code{quality.data}] a data.frame containing information about quality
scores with fields \code{name}, \code{label}, \code{score} as
generated by function \code{\LinkA{qscore.summary}{qscore.summary}}
\item[\code{dir.out}] absolute path of a directory where the file is
generated (defaults to the current directory)
\item[\code{array.name}] name or identifier of the array
\item[\code{x}] a variable name from \code{arrayCGH\$cloneValues} giving the order position
of the clones along the genome (defaults to 'PosOrder')
\item[\code{y}] a vector of one or two variable names to be passed to \code{\LinkA{report.plot}{report.plot}}
\item[\code{chrLim}] an optional variable name from \code{arrayCGH\$cloneValues}
giving the limits of each chromosome
\item[\code{ylim}] a numeric vector of length 2 to be passed to
\code{\LinkA{report.plot}{report.plot}}: y axis range of the genomic profile display
\item[\code{clim}] a numeric vector of length 2 to be passed to
\code{\LinkA{report.plot}{report.plot}}: color range of the genomic profile
\item[\code{zlim}] a numeric vector of length 2 to be passed to
\code{\LinkA{report.plot}{report.plot}}: color range for array image display
\item[\code{intensity}] an optional list with names c("M.var", "A.var",
"pred.var", "span"). The first 3 items specify existing variable names
from \code{arrayCGH\$arrayValues} that will be used to draw a
MA-plot. The last item is the value of the loess 'span'
\item[\code{light}] boolean value: if (light), only the core of the html file
is generated; if (!light), a complete html file is generated
\item[\code{file.name}] file name of the generated report (defaults to
"report")
\item[\code{width}] plot width, in inches
\item[\code{height}] plot height, in inches
\item[\code{...}] further arguments to be passed to \code{\LinkA{report.plot}{report.plot}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function creates an HTML report file showing
- the array image and the genome representation before normalization
(if \code{array.nonorm} is provided) and after normalization, and
optionally a MA-plot
- a table with information about the number of flagged spots for each
flag, and the number of remaining spots after normalization
- a table with information about various quality criteria for the
array

In order
\end{Details}
\begin{Value}
none
\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{flag.summary}{flag.summary}}, \code{\LinkA{report.plot}{report.plot}}
\end{SeeAlso}

