\HeaderA{calcPBChiSquare}{Probability binning metirc for comparing the probability binned
datasets}{calcPBChiSquare}
\keyword{misc}{calcPBChiSquare}
\begin{Description}\relax
This function calculates the Probability binning metric proposed by
Baggerly et al. The function utilizes the data binned using the
\code{proBin} and \code{binByRef} functions.
\end{Description}
\begin{Usage}
\begin{verbatim}
calcPBChiSquare(ctrlRes,sampRes,ctrlCount,sampCount)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ctrlRes}] The result generated by calling the \code{probBin}
function on a control dataset.
\item[\code{sampRes}] The result generated by calling the \code{byByRef}
function on a test sample dataset
\item[\code{ctrlCount}] The number of events in the control sample
\item[\code{sampCount}] The number of events in the test sample being compared
\end{ldescription}
\end{Arguments}
\begin{Value}
A list containing the statistic, p.value, observed, expected counts and 
the residuals
\end{Value}
\begin{Author}\relax
Nishant Gopalakrishnan
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{proBin}{proBin}}, \code{\LinkA{calcPBChiSquare}{calcPBChiSquare}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(GvHD)
# flow frame 1 is treated as  control dataset and used to generate bins
resCtrl<-proBin(GvHD[[1]][,c("FSC-H","SSC-H","Time")],200)  
plotBins(resCtrl,GvHD[[1]],channels=c("FSC-H","SSC-H","Time"),title="Binned control data")
# Same bins are applied to flowFrame 16
resSample<-binByRef(resCtrl,GvHD[[16]][,c("FSC-H","SSC-H","Time")])
ctrlCount<-nrow(GvHD[[1]])
sampCount<-nrow(GvHD[[16]])
stat<-calcPBChiSquare(resCtrl,resSample,ctrlCount,sampCount)
\end{ExampleCode}
\end{Examples}

