\HeaderA{ecoligenome.operon}{Known operon in E.coli - data.frame}{ecoligenome.operon}
\keyword{datasets}{ecoligenome.operon}
\begin{Description}\relax
The known operon in the Escherichia coli genome.
\end{Description}
\begin{Usage}
\begin{verbatim}data(ecoligenome.operon)\end{verbatim}
\end{Usage}
\begin{Format}\relax
A data frame with 932 observations (genes) on the following 4 variables.
\describe{
\item[gene.name] a character vector
\item[gene.annotation] a character vector
\item[operon.name] a factor with levels the names of the operons
\item[operon.comments] a factor with levels the comments for the operons
}
\end{Format}
\begin{Details}\relax
For some operons, the source of information specifies the existence of
regulating elements such as promoter, terminator, box, etc\ldots
In those cases, the \code{gene.name} is set to \code{"Regulation"},
and the \code{gene.annotation} gives what kind of regulating element
it is. If volonteers, it would be neat to map those on the genome\ldots
Besides that, not much to add. The data structure is fairly straightforward.
\end{Details}
\begin{Source}\relax
Built from the webpage:
\url{http://www.cib.nig.ac.jp/dda/backup/taitoh/ecoli.operon.html}
\end{Source}
\begin{Examples}
\begin{ExampleCode}
library(Biobase)
data(ecoligenome.operon)
data(ecoligenomeSYMBOL2AFFY)

## something that might be useful when working with Affymetrix data:
## get the Affymetrix identifiers for the probe sets bundled in operons
## (see the vignette for more details)
ecoligenome.operon$affyid <-
unname(unlist(mget(ecoligenome.operon$gene.name,
                   ecoligenomeSYMBOL2AFFY, ifnotfound=NA)))

\end{ExampleCode}
\end{Examples}

