\HeaderA{quadrantGate}{Automated quad gating}{quadrantGate}
\begin{Description}\relax
This function tries to find the most likely separation of
two-dimensional flow cytometry in four quadrants.
\end{Description}
\begin{Usage}
\begin{verbatim}
quadrantGate(x, stains, alpha=c("min", "min"), sd=c(2, 2), plot=FALSE,
filterId="defaultQuadGate", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A \code{\LinkA{flowSet}{flowSet}} or
\code{\LinkA{flowFrame}{flowFrame}}. 
\item[\code{stains}] A character vector of length two giving the two flow
parameters for which the quad gate is to be computed. 
\item[\code{alpha, sd}] Tuning factors to control the computation of the
gate boundaries. See \code{\LinkA{rangeGate}{rangeGate}} for details. 
\item[\code{plot}] Logical. Produce plots of intermediate results. 
\item[\code{filterId}] Character, the name assigned to the resulting
filter. 
\item[\code{...}] Additional arguments 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The most likely separation between postitive and negative stains for
two-dimensional data is computed based on density
estimates. Essentially, the gate parameters are first fitted
separately for the two parameters and later combined. See the
documentation for \code{\LinkA{rangeGate}{rangeGate}} for details. There is a
certain amount of heuristics involved in this process. The algorithm
can be slightly tweaked using the \code{alpha} and \code{sd}
arguments. Their values will be recycled for the two dimensions unless
explicitely given as vectors of length 2.
\end{Details}
\begin{Value}
An object of class \code{\LinkA{quadGate}{quadGate}}.
\end{Value}
\begin{Author}\relax
Florian Hahne
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{quadGate}{quadGate}},
\code{\LinkA{rangeGate}{rangeGate}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(GvHD)
dat <- GvHD[pData(GvHD)$Patient==10]
dat <- transform(dat, "FL4-H"=asinh(`FL4-H`), "FL2-H"=asinh(`FL2-H`))
qg <- quadrantGate(dat, c("FL2-H", "FL4-H"))
qg
if(require(flowViz))
xyplot(`FL2-H`~`FL4-H`, dat, filter=qg)
qg <- quadrantGate(dat, c("FL2-H", "FL4-H"), alpha=c(0.1, 0.9), plot=TRUE)

\end{ExampleCode}
\end{Examples}

