\name{predictionRegion}
\alias{predictionRegion}
\alias{predictionRegion,CNSet,integer-method}
\title{Prediction regions for integer copy number}
\description{Bivariate normal prediction regions for integer copy
number.  Copy numbers 0-4 allowed.}
\usage{
predictionRegion(object, copyNumber)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{object}{A \code{CNSet} object.}
\item{copyNumber}{Integer vector.  0-4 allowed.}
}
\details{

We fit a linear regression for each allele to the diallic genotype
cluster medians.  Denoting the background and slope by nu and phi,
respectively, the mean for the bivariate normal prediction region is
given by

mu_A = nu_A + CA * phi_A

and

mu_B nu_B + CB * phi_B

The variance and correlation of the normalized intensities is
estimated from the diallelic genotype clusters AA, AB, and BB on the
log-scale.  For copy number not equal to two, we assume that the
variance is approximately the same for copy number not equal to 2.

}

\value{

A list named by the genotype.  NULL' refers to copy number zero, A'
is a hemizygous deletion, etc. Each element is a list of the means
(mu) and covariance (cov) for each marker stored as an array.  For
mu', the dimensions of the array are marker x allele (A or B) x
batch.  For cov', the dimensions of the array are marker x 3
(varA, cor, and varB) x batch.

}

\references{
Scharpf et al., 2011, Biostatistics.
}
\author{
R. Scharpf
}

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

\seealso{
\keyword{list}