\name{getTopTable}
\alias{getTopTable}
%\alias{getTopTable,cellHTS-method}

\title{Generate the hit list from a scored cellHTS object}
 
\description{
  Generate the hit list from a scored {\linkS4class{cellHTS}} object and write it to a tab-delimited file.
}


\usage{
getTopTable(cellHTSlist, file="topTable.txt", verbose=interactive())
}

\arguments{
  \item{cellHTSlist}{a list of \code{\linkS4class{cellHTS}} objects. See details.}
  \item{file}{the name of the output file. Default is "topTable.txt".}
  \item{verbose}{a logical value, if \code{TRUE}, the function reports its progress. Defaults to the state of \code{\link[base:interactive]{interactive()}}.}
}

\details{
Argument \code{cellHTSlist} should be a list containing at least one component named "scored" which corresponds 
to a scored \code{\linkS4class{cellHTS}} object. Other possible components of \code{cellHTSlist} can be:
\itemize{
\item \code{"raw"}: a \code{cellHTS} object containing unpreprocessed data. I.e. \code{state(cellHTSlist[["raw"]])["normalized"]=FALSE}.
\item \code{"normalized"}: a \code{cellHTS} object containing normalized data. I.e. \code{state(cellHTSlist[["normalized"]])["normalized"]=TRUE} and \code{state(cellHTSlist[["normalized"]])["scored"]=FALSE}.
}

All of the components of \code{cellHTSlist} should be \code{cellHTS} objects containing data from the same experiment, but in different preprocessing stages. 

This function generates a \code{data.frame} that is written to \code{file}. 
This data.frame and the output file contain the list of scored probes 
ordered by decreasing score values. They have one row for each well and plate, 
and contain the following columns (depending on the components of \code{cellHTSlist}):

\itemize{

\item \code{plate}: plate identifier for each well.

\item \code{position}: gives the position of the well in the plate (ranges from 1 to the total 
number of wells in the plate).

\item \code{well}: gives the alphanumeric identifier for the wells.

\item \code{score}: content of slot \code{assayData} of the scored \code{\linkS4class{cellHTS}} object given in \code{cellHTSlist[["scored"]]}.

\item \code{wellAnno}: well annotation as given by the plate configuration file.

\item \code{finalWellAnno}: Gives the final well annotation for the scored values.
    It combines the information given in the plate configuration file with the values in \code{assayData} slot of the scored \code{cellHTS} object, in order to have into account the wells that have been flagged either by the screen log file, or manually by the user during the analysis. These flagged wells appear with the annotation \emph{flagged}.

\item \code{raw_ri_chj}: (if \code{cellHTSlist[["raw"]]} is given) contains the raw intensities for replicate \code{i} in channel \code{j} (content of slot \code{assayData} of the \code{cellHTS} object given in \code{cellHTSlist[["raw"]]}).

\item \code{median_chj}: (if \code{cellHTSlist[["raw"]]} is given) corresponds to the median of raw measurements across replicates in channel \code{j}.

\item \code{diff_chj}: (if \code{cellHTSlist[["raw"]]} is given and if there are two replicates or samples) gives the difference between replicate (sample) raw measurements in channel \code{j}.

\item \code{average_chj}: (if \code{cellHTSlist[["raw"]]} is given and if there are more than 2 replicates or samples) corresponds to the average between replicate raw intensities for channel \code{j}.

\item \code{raw/PlateMedian_ri_chj}: (if \code{cellHTSlist[["raw"]]} is given) this column gives the ratio between each raw measurement and the median intensity in each plate for replicate (or sample) \code{i} in channel \code{j}. The plate median is determined for the raw intensities using exclusively the wells annotated as \code{sample}.

\item \code{normalized_ri_chj}: (if \code{cellHTSlist[["normalized"]]} is given) gives the normalized intensities 
for replicate (sample) \code{i} in channel \code{j}. This corresponds to the content of slot \code{assayData} of 
the \code{cellHTS} object given in \code{cellHTSlist[["normalized"]]}.

} 

Additionally, if the \code{cellHTS} object given in \code{cellHTSlist[["scored"]]} is already annotated, the output \code{topTable} also contains the gene annotation stored in slot \code{featureData}.
}

\value{
Generates the file with the hit list and outputs a \code{\link{data.frame}} with the same contents.
}

\seealso{\code{\linkS4class{cellHTS}}}

\references{
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, \emph{Genome Biology} \bold{7}, R66.
}


\author{Ligia P. Bras \email{ligia@ebi.ac.uk}}

\examples{
    data(KcViabSmall)
    xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none") 
    xsc <- scoreReplicates(xn, sign="-", method="zscore")
    xsc <- summarizeReplicates(xsc, summary="mean")
    out <- getTopTable(cellHTSlist=list("raw"=KcViabSmall, "normalized"=xn, "scored"=xsc), file=tempfile())
}
\keyword{manip}