\name{methylationCall}
\alias{methylationCall}

\title{ Estimated methylation call }

\description{
Estimated methylation call based on the fitting results of \code{\link{gammaFitEM}}
}

\usage{
methylationCall(x, threshold = 0.95, ...)
}

\arguments{
	\item{x}{ a vector of M-values covering the whole genome or a "gammaFit" class object returned by \code{\link{gammaFitEM}} }
	\item{threshold}{the probability threshold to make a methylation call. The threshold can be a vector of two: unmethylation threshold and methylation threshold}
	\item{\dots}{ other parameters used by \code{\link{gammaFitEM}} }
}
\details{
	Retrieve the probability element returned by \code{\link{gammaFitEM}}, and convert it as three status calls based on probability threshold
}
\value{
A vector of three methylation status: "Unmethy" (unmethylation posterior probability > unmethylation threshold), "Methy" (methylation posterior probability > methylation threshold), or "Margin". The sum of unmethylation posterior probability and methylation posterior probability equals one. The methylation probability is returned as an attribute of "probability".
}
\references{

}
\author{ Pan DU }

\seealso{
\code{\link{gammaFitEM}}
}

\examples{
data(example.lumiMethy)
M <- exprs(example.lumiMethy)
fittedGamma <- gammaFitEM(M[,1], initialFit=NULL, maxIteration=50, tol=0.0001, plotMode=TRUE, verbose=FALSE)
methyCall <- methylationCall(fittedGamma)
table(methyCall)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{methods}