\inputencoding{latin1}
\HeaderA{as.profileCGH}{Create an object of class profileCGH}{as.profileCGH}
\methaliasA{as.profileCGH.data.frame}{as.profileCGH}{as.profileCGH.data.frame}
\keyword{manip}{as.profileCGH}
\begin{Description}\relax
Create an object of class profileCGH.
\end{Description}
\begin{Usage}
\begin{verbatim}
as.profileCGH(object,...)
## S3 method for class 'data.frame':
as.profileCGH(object, infaction=c("value","empty"), value=20, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] A data.frame to be convert into profileCGH.
\item[\code{infaction}] If "value" then the LogRatio with infinite values
(-Inf, Inf) are replace by + or - \code{value} according to the sign. If "empty"
then NAs are put instead.
\item[\code{value}] replace Inf by \code{value} if \code{infaction} is
"value".
\item[\code{...}] 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The data.frame to be convert must at least contain the
following fields: LogRatio, PosOrder, and Chromosome. If the field
Chromosome is of mode character,  it is automatically converted into a
numeric vector (see \code{\LinkA{ChrNumeric}{ChrNumeric}}); a field ChromosomeChar
contains the character labels. The data.frame to be converted into a
profileCGH objet is split into two data.frame: profileValuesNA contains
the rows for which there is at least a missing value for either
LogRatio, PosOrder or Chromosome; profileValues contains the remaining rows.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{ }] A list with the following attributes
\item[\code{profileValues}] A data.frame
\item[\code{profileValuesNA}] A data.frame
\end{ldescription}
\end{Value}
\begin{Note}\relax
People interested in tools dealing with array CGH analysis can
visit our web-page \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Philippe Hupé, \email{glad@curie.fr}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{as.data.frame.profileCGH}{as.data.frame.profileCGH}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(snijders)

### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)

attributes(profileCGH)

\end{ExampleCode}
\end{Examples}

