\name{screenMatch}
\alias{screenMatch}
\title{Matching the gene annotation of two screens}
\description{
Match the annotation of two \code{cellHTS} objects in order to find the common 
gene-perturbing reagents  
}
\usage{
screenMatch(screens, ids)
}
\arguments{
  \item{screens}{a list of annotated cellHTS objects.}
  \item{ids}{a character vector of length two giving, for each cellHTS object, the name of the column of slot 'geneAnno' that should be used for the annotation IDs. See details.}
}

\details{
By default, if \code{ids} is missing, the column \code{GeneID} of the slot \code{geneAnno} of each of the \code{cellHTS} objects in \code{screens} is taken for the annotation IDs when comparing the two data sets.
}

\value{
A list with two components:
\item{p.overlap}{a vector giving the proportion of overlap in the screens' annotation.}
\item{isInBoth}{a list of logical vectors, each of which with length equal to the product between \code{nr. Well} and \code{nr. Plates} in each screen, indicating whether the respective gene-perturbing reagent of that screen is also present in the other.}
}

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

\examples{
    ## Just for exemplification purposes, we consider the complete genome-wide screen "KcViab" 
    ## and its first 3 plates ("KcViabSmall"): 
    data(KcViab)
    data(KcViabSmall)
    screens <- list(KcViab, KcViabSmall)
    out <- screenMatch(screens)
    out$p.overlap
    sapply(out$isInBoth, sum)
    sapply(1:2, function(z) table(screens[[z]]$geneAnno$Plate[out$isInBoth[[z]]]))
}

\keyword{manip}