\name{posteriorProbability}
\alias{posteriorProbability}
\alias{posteriorProbability,CNSet-method}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Calculate the posterior probability for integer copy numbers.}

\description{
Calculate the posterior probability for integer copy numbers using the
bivariate normal prediction regions.
}

\usage{
posteriorProbability(object, predictRegion, copyNumber = 0:4, w)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{object}{
A \code{CNSet} object.
}
\item{predictRegion}{
A list containing the bivariate normal prediction region for each of
the possible genotypes.
}
\item{copyNumber}{
Integer vector.
}

\item{w}{ numeric vector of prior probabilities for each of the copy
number states.  Must be the same length as \code{copyNumber} and sum
to 1.}

}

\details{
This is currently under development.
}

\value{
An array (features x samples x copy number)
}

\author{
R. Scharpf
}

\note{
This is under development. Use at your own risk.
}

%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
}
\examples{
data(cnSetExample)
pr <- predictionRegion(cnSetExample, copyNumber=0:4)
pp <- posteriorProbability(cnSetExample, predictRegion=pr)
dim(pp)

## multiple batches
data(cnSetExample2)
pr <- predictionRegion(cnSetExample2, copyNumber=0:4)
pp <- posteriorProbability(cnSetExample2, predictRegion=pr)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{array}