\HeaderA{export.filter}{Export filter data as text files}{export.filter}
\keyword{manip}{export.filter}
\begin{Description}\relax
Export data from classes \code{\LinkA{FilterTreeSet}{FilterTreeSet}} or \code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}} to \code{outfile}.
\end{Description}
\begin{Usage}
\begin{verbatim}
export.filter(xps.fltr, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{xps.fltr}] an object of type \code{\LinkA{FilterTreeSet}{FilterTreeSet}} or \code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}}.
\item[\code{treename}] tree name to export.
\item[\code{treetype}] type of tree(s) to export, 'pfr', 'ufr' or 'stt'.
\item[\code{varlist}] names of tree leaves to export.
\item[\code{outfile}] name of output file.
\item[\code{sep}] column separator
\item[\code{as.dataframe}] if \code{TRUE} a data.frame will be returned.
\item[\code{verbose}] logical, if \code{TRUE} print status information.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Export data from classes \code{\LinkA{FilterTreeSet}{FilterTreeSet}}, or \code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}}
to \code{outfile}.

Parameter \code{varlist} lists the parameters to export: \\
- parameters are separated by ":", e.g. \code{varlist="fUnitName:fFlag"}. \\
- for \code{varlist="*"} all valid parameters will be exported.

For class \code{FilterTreeSet} the following \code{varlist} parameters are valid:
\Tabular{lll}{
& \code{fUnitName}:& unit name (probeset ID). \\
& \code{fFlag}:& mask.
}

For class \code{AnalysisTreeSet} \code{varlist} can contain annotation
parameters and parameters of the resulting data. \\
Following \code{varlist} annotation parameters are valid:
\Tabular{lll}{
& \code{fUnitName}:& unit name (probeset ID). \\
& \code{fTranscriptID}:& transcript\_id (probeset ID). \\
& \code{fName}:& gene name. \\
& \code{fSymbol}:& gene symbol. \\
& \code{fAccession}:& mRNA accession such as Refseq ID. \\
& \code{fEntrezID}:& entrez ID. \\
& \code{fChromosome}:& chromosome. \\
& \code{fStart}:& start position. \\
& \code{fStop}:& stop position. \\
& \code{fStrand}:& strand on chromosome. \\
& \code{fCytoBand}:& cytoband.
}
For class \code{AnalysisTreeSet} the following \code{varlist} parameters are valid:
\Tabular{lll}{
& \code{mn1}:& mean of group 1. \\
& \code{mn2}:& mean of group 2. \\
& \code{fc}:& fold-change fc=mn2/mn1. \\
& \code{se}:& standard error. \\
& \code{df}:& degree of freedom. \\
& \code{stat}:& t-statistic. \\
& \code{pval}:& p-value. \\
& \code{nper}:& number of permutations. \\
& \code{pcha}:& p-chance. \\
& \code{padj}:& adjusted p-value. \\
& \code{flag}:& flag. \\
& \code{mask}:& only rows with \code{flag=1} will be exported.
}
\end{Details}
\begin{Value}
If \code{as.dataframe} is \code{TRUE}, the data will be imported into the
current R session as \code{data.frame}. Otherwise, \code{NULL} will be returned.
\end{Value}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{export-methods}{export.Rdash.methods}}
\end{SeeAlso}

