\HeaderA{link.genes}{Links for a list of genes}{link.genes}
\keyword{IO}{link.genes}
\keyword{file}{link.genes}
\begin{Description}\relax
Generates a htmlpage with links to several public repositories for a list of genes.
\end{Description}
\begin{Usage}
\begin{verbatim}
  link.genes(genenames, filename, ll = FALSE, refseq = TRUE, symbol = TRUE,
    omim = TRUE, ug = TRUE, chipname = "", cdfname = NULL, dataframe = NULL,
    title = NULL, bg.col = "white", text.col = "black", link.col = "blue", 
    tableborder = 1, new.window = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genenames}] a character vector containing the names of the interesting genes
\item[\code{filename}] a character string naming the file in which the output should be stored.
Must have the suffix ".html"
\item[\code{ll}] logical indicating if Locus Links should be added to the output
\item[\code{refseq}] logical indicating if RefSeq links should be added to the output
\item[\code{symbol}] logical indicating if the gene symbols should be added to the output
\item[\code{omim}] logical indicating if OMIM links should be added to the output
\item[\code{ug}] logical indicating if UniGene links should be added to the output
\item[\code{chipname}] character string specifying the chip type used in the analysis. Must
be specified as in the meta-data section of Bioconductor (e.g., \code{"hgu133a"}
for the Affymetrix HG-U133A chip). Need not to be specified if \code{cdfname}
is specified
\item[\code{cdfname}] character string specifying the cdf name of the used chip. Must exactly follow
the nomenclatur of the Affymetrix chips (e.g., \code{"HG-U133A"} for the
Affymetrix HG-U133A chip). If specified, links to the Affymetrix webpage for the
interesting genes will be added to the output
\item[\code{dataframe}] matrix having one row for each interesting gene, i.e.\ \code{nrow(dataframe)}
must be equal to \code{length(genenames)}. This matrix contains additional information 
on the list of genes that should be added to the output. If \code{NULL} (default) no
information will be added to the link list
\item[\code{title}] character string naming the title that should be used in the html page
\item[\code{bg.col}] specification of the background color of the html page. See \code{?par} for
how colors can be specified
\item[\code{text.col}] specification of the color of the text used in the html page. See \code{?par} for
how colors can be specified
\item[\code{link.col}] specification of the color of the links used in the html file. See \code{?par}
for how colors can be specified
\item[\code{tableborder}] integer specifying the thickness of the border of the table
\item[\code{new.window}] logical indicating if the links should be opened in a new window
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}}, \code{\LinkA{sam}{sam}}, \code{\LinkA{link.siggenes}{link.siggenes}}, \code{\LinkA{sam2html}{sam2html}}
\end{SeeAlso}