\name{estimateMethylationBG}
\alias{estimateMethylationBG}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Estimate the background levels of Illumina Infinium methylaton microarrays
}
\description{
Estimate the background levels of Illumina Infinium methylaton microarrays. It is called by function \code{\link{bgAdjustMethylation}}
}
\usage{
estimateMethylationBG(methyLumiM, separateColor = FALSE, nbin = 1000)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{methyLumiM}{a MethyLumiM object or any eSet object with "methylated" and "unmethylated" data matrix element in the assayData slot }
  \item{separateColor}{determine whether to separately process two color channels}
  \item{nbin}{ the number of bins in the histogram used to estimate the mode position of the density }
}
\details{
The estimation of background level of Infinium methylaton microarray is based on the assumption that the lots of CpG sites are unmethylated, which results in a density mode of the intensities measured by methylated probes. The position of this mode represents the background level.
}
\value{
a vector of estimated background levels for individual samples.
}
\references{
}
\author{
Pan DU
}

\seealso{
See Also \code{\link{lumiMethyB}} and \code{\link{bgAdjustMethylation}}
}
\examples{
data(example.lumiMethy)
estimatedBG = estimateMethylationBG(example.lumiMethy)
estimatedBG
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{methods}