\name{configure}
\alias{configure}
\alias{configure.cellHTS}
\title{Configures the plates and plate result files}
\description{
  Annotate the plates and the plate result files of a given \code{cellHTS} object.  
}
\usage{
configure(x, \dots)
\method{configure}{cellHTS}(x, confFile, logFile, descripFile, path, \dots)
}
\arguments{
  \item{x}{a \code{cellHTS} object.}
  \item{confFile}{the name of the configuration file (see details).
    This argument is just passed on to the \code{\link{read.table}}
    function, so any of the valid argument
    types for \code{\link{read.table}} are valid here, too. Must contain one row for each well and each batch.}
  \item{logFile}{optional; the name of the screen log file (see details).
    This argument is just passed on to the \code{\link{read.table}}
    function, so any of the valid argument
    types for \code{\link{read.table}} are valid here, too.}
  \item{descripFile}{the name of the screen description file (see details).
    This argument is just passed on to the \code{\link{readLines}}
    function, so any of the valid argument
    types for \code{\link{readLines}} are valid here, too.}
  \item{path}{optional; a character of length one indicating the path in
    which to find the configuration files. Useful when the files are locate in the same directory, 
    but should be omitted otherwise.}
  \item{\dots}{additional parameters - ignored.}
}

\details{
  \itemize{
    \item{confFile}{This file is expected to be a tab-delimited file with
    at least three columns, and column names \code{Batch}, \code{Well} and
    \code{Content}. The contents of \code{Batch} are expected to be integer.} 
    \item{logFile}{If given as an argument, it is expected to be a
    tab-delimited file with at least three columns, and column names
    \code{Filename}, \code{Well}, and \code{Flag}. Further columns are allowed.}
    \item{descripFile}{This file is the screen description file with
    general information about the screen.}
  }
  
Data from wells that are annotated as \emph{empty} are ignored and are set to NA in \code{x} in slot \code{xraw}.  
}

\value{
 An S3 object of class \code{cellHTS}, which extends the argument \code{x} by the following elements:
 \item{plateConf}{a data.frame containing what was read from input file \code{confFile}. The number of rows is equal to the product between the number of wells in each plate and the number of batches.}
 \item{screenLog}{a data.frame containing what was read from input file \code{logFile}.}
 \item{screenDesc}{object of class \code{character} containing what was read from input file \code{descripFile}.}
Moreover, the processing status of the \code{cellHTS} object is updated in the slot \code{state} to \code{state["configured"]=TRUE}.
 \item{wellAnno}{object of class \code{factor} of length number of plates x number of wells per plate, with possible levels: \emph{empty}, \emph{other}, \emph{neg}, \emph{sample}, and \emph{pos}, indicative of the contents of the wells. Other levels may be employed for the positive and negative controls, besides \emph{pos} and \emph{neg}.}

There are methods \code{print.cellHTS}, \code{configure.cellHTS} and \code{annotate.cellHTS}.}

\seealso{
  \code{\link[cellHTS:readPlateData]{readPlateData}}
}

\author{Wolfgang Huber \email{huber@ebi.ac.uk}, Ligia Braz \email{ligia@ebi.ac.uk}}

\references{..}

\examples{
\dontrun{
    datadir <- system.file("KcViabSmall", package = "cellHTS")
    x <- readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
    x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)
}
}
\keyword{manip}