\HeaderA{metaProbesets}{Create MetaProbeset File for APT}{metaProbesets}
\keyword{manip}{metaProbesets}
\begin{Description}\relax
Create MetaProbeset File for APT function \dQuote{apt-probeset-summarize}.
\end{Description}
\begin{Usage}
\begin{verbatim}
metaProbesets(xps.scheme, infile = character(0), outfile = character(0), exonlevel="metacore")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{xps.scheme}] exon \code{SchemeTreeSet}.
\item[\code{infile}] Name of file containing exon transcript\_cluster\_ids.
\item[\code{outfile}] Name of resulting file containing meta probeset definitions.
\item[\code{exonlevel}] exon annotation level determining which probes should be used.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function allows to create a metaprobeset file for APT function \dQuote{apt-probeset-summarize}
to be used with option \dQuote{-m}. The \code{infile} must contain exon transcript\_cluster\_ids,
one per line, e.g. one can export the \code{rownames(data.rma)} \\
The resulting file may be useful if you want to compare results created with \code{xps} to results
created with APT function \dQuote{apt-probeset-summarize}.
\end{Details}
\begin{Value}
None.
\end{Value}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
## first, load ROOT exon scheme file:
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/"))

metaProbesets(scheme.exon,"metacore.txt","metacoreList.mps","metacore")
## End(Not run)
\end{ExampleCode}
\end{Examples}

