\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{ } \value{ An array (features x samples x copy number) } \author{ R. Scharpf } \note{ %Remark about nonpolymorphic probes } %% ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ \code{\link{predictionRegion}}, \code{\link{genotypes}}, \code{\link{calculatePosteriorMean}} } \examples{ data(sample.CNSet) pr <- predictionRegion(sample.CNSet, copyNumber=0:4) pp <- posteriorProbability(sample.CNSet, predictRegion=pr) dim(pp) ## multiple batches data(sample.CNSet2) pr <- predictionRegion(sample.CNSet2, copyNumber=0:4) pp <- posteriorProbability(sample.CNSet2, predictRegion=pr) } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. \keyword{array}