man/posteriorProbability.Rd
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 \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{
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 posteriorProbability(object, predictRegion, copyNumber = 0:4, w)
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 }
 %- 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.
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   }
 
   \item{w}{ numeric vector of prior probabilities for each of the copy
     number states.  Must be the same length as \code{copyNumber} and sum
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     to 1.}
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 }
 
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 \details{
 This is currently under development.
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 }
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 \value{
 An array (features x samples x copy number)
 }
 
 \author{
 R. Scharpf
 }
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 \note{
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   This is under development. Use at your own risk.
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 }
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
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   \code{\link{predictionRegion}}, \code{\link{genotypes}} %\code{\link{calculatePosteriorMean}}
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 }
 \examples{
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 data(cnSetExample)
 pr <- predictionRegion(cnSetExample, copyNumber=0:4)
 pp <- posteriorProbability(cnSetExample, predictRegion=pr)
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 dim(pp)
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 ## multiple batches
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 data(cnSetExample2)
 pr <- predictionRegion(cnSetExample2, copyNumber=0:4)
 pp <- posteriorProbability(cnSetExample2, predictRegion=pr)
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 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the
 % R documentation directory.
 \keyword{array}