\HeaderA{annotate}{Annotates the gene IDs of a given cellHTS object}{annotate}
\methaliasA{annotate.cellHTS}{annotate}{annotate.cellHTS}
\keyword{manip}{annotate}
\begin{Description}\relax
Annotate the gene IDs of a given cellHTS object.
\end{Description}
\begin{Usage}
\begin{verbatim}
annotate(x, ...)
## S3 method for class 'cellHTS':
annotate(x, geneIDFile, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a cellHTS object.
\item[\code{geneIDFile}] the name of the file with the gene IDs (see details).
This argument is just passed on to the \code{\LinkA{read.table}{read.table}}
function, so any of the valid argument
types for \code{\LinkA{read.table}{read.table}} are valid here, too. Must contain one row for each well and each plate.
\item[\code{...}] additional parameters - ignored.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\item[geneIDFile] This file is expected to be a tab-delimited file with at least three columns, and column names \code{Plate}, \code{Well} and \code{GeneID}. The contents of \code{Plate} are expected to be integer. Further columns are allowed.
\end{Details}
\begin{Value}
An S3 object of class \code{cellHTS}, which extends the argument \code{x} by the following element:
\begin{ldescription}
\item[\code{geneAnno}] a data.frame containing what was read from input file \code{geneIDFile}. 
The number of rows is equal to the product between the number of wells in each plate and the number of plates.
\end{ldescription}


Moreover, the processing status of the \code{cellHTS} object is updated in the slot \code{state} to \code{state["annotated"]= TRUE}.
There are methods \code{print.cellHTS}, \code{configure.cellHTS} and \code{annotate.cellHTS}.
\end{Value}
\begin{Author}\relax
Wolfgang Huber \email{huber@ebi.ac.uk}, Ligia Braz \email{ligia@ebi.ac.uk}
\end{Author}
\begin{References}\relax
..
\end{References}
\begin{Examples}
\begin{ExampleCode}
 datadir = system.file("KcViabSmall", package = "cellHTS")
 x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
 confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
 logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
 descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
 x = configure(x, confFile, logFile, descripFile)
 geneIDFile = system.file("KcViabSmall", "GeneIDs.txt", package="cellHTS")
 x = annotate(x, geneIDFile)
\end{ExampleCode}
\end{Examples}

