\HeaderA{mapGeneInfo}{Creating URL strings for external database links}{mapGeneInfo}
\aliasA{SFGL}{mapGeneInfo}{SFGL}
\aliasA{UCBFGL}{mapGeneInfo}{UCBFGL}
\aliasA{URLstring}{mapGeneInfo}{URLstring}
\aliasA{widget.mapGeneInfo}{mapGeneInfo}{widget.mapGeneInfo}
\keyword{manip}{mapGeneInfo}
\begin{Description}\relax
These functions are used with \code{\LinkA{htmlPage}{htmlPage}}.
The function \code{mapGeneInfo}, takes all the arguments and generate
a character matrix of two columns.  The first columns representing the
name of the argument and the second columns represents the value of an
argument. 
The function \code{widget.mapGeneInfo} allows the user to enter this
information  interactively.
\end{Description}
\begin{Usage}
\begin{verbatim}
mapGeneInfo(widget = FALSE, Gnames, Name = "pubmed", ID =
                 "genbank", ACC = "SMDacc", ...)
widget.mapGeneInfo(Gnames) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{widget}] A logical value specifying if widgets should be used.
\item[\code{Name}] The external database for spot description, E.g. "pubmed".
\item[\code{ID}] The external database for spot ID, E.g. "operon", "Riken", "locuslink".
\item[\code{ACC}] The external database for gene accession number, E.g. "genebank".
\item[\code{Gnames}] An object of class \code{matrix}, \code{data.frame} or \code{marrayInfo}
which contains  description of spotted probe sequences.
\item[\code{...}] Other column names
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function \code{mapGeneInfo} generates a character matrix with the
first column representing the column headings of "Gnames" and the
second column representing the corresponding names in the list
\code{URLstring}.  For example, if a particular column in "Gnames"
with column names "ID" contains genebank accession number, then the
function \code{mapGeneInfo} generates a row containing "ID" in the
first column and "genbank" in the second.  Examples are \code{SFGL}
and \code{UCBFGL}.\\

\code{URLstring} is a list contains the URL to various external
database, E.g. operon, Riken, genbank. \\
The current choices are: 
"pubmed",  "locuslink",  "riken",   "SMDclid",    "SMDacc",    "operonh2",  "operonh1" ,
"operonm2",  "operonm1" and  "genbank" .  
"SMDclid" and "SMDacc" are links to Stanford Microarray Databases.
\end{Details}
\begin{Author}\relax
Jean Yee Hwa Yang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
 mapGeneInfo(ID="genebank", ll="locuslink")
 mapGeneInfo(ID="locuslink", Sample.ID="riken")
\end{ExampleCode}
\end{Examples}