\HeaderA{write.sgr}{Write Affy IGB .sgr format files}{write.sgr}
\keyword{IO}{write.sgr}
\begin{Description}\relax
The affy Integrated Genome Browser (IGB) is a powerful, fast browser
for genomic data.  The file format is simple (three columns:
chromosome, location, and score) to generate.  This function will
write the sgr files associated with a aGFFcalc object.  There will be
either one or two files (default two) representing the raw data and
the calculated data (which is output as -log10(val) for visualization
purposes).
\end{Description}
\begin{Usage}
\begin{verbatim}
write.sgr(agff, raw = TRUE, vals = TRUE, directory = ".")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{agff}] An aGFFCalc object obtained after running do.aGFF.calc
\item[\code{raw}] Create a file for the raw data?
\item[\code{vals}] Create a file for the calculated p-values?
\item[\code{directory}] Give a directory for storing the files
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Sean Davis
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(example.agff)
write.sgr(example.agff)
\end{ExampleCode}
\end{Examples}

