\name{mosaicsPeak}
\alias{mosaicsPeak}
\alias{mosaicsPeak,MosaicsFit-method}
\title{
Call peaks based on fitted MOSAiCS model
}
\description{
Call peaks using \code{MosaicsFit} class object, which is a fitted MOSAiCS model.
}
\usage{
mosaicsPeak( object, ... )
\S4method{mosaicsPeak}{MosaicsFit}( object, signalModel="2S", FDR=0.05, maxgap=200, minsize=50, thres=10 )
}
%- maybe also 'usage' for other objects documented here.
\arguments{
    \item{object}{Object of class \code{MosaicsFit},
        a fitted MOSAiCS model obtained using function \code{mosaicsFit}. }
    \item{signalModel}{Signal model.
        Possible values are "1S" (one-signal-component model) and
        "2S" (two-signal-component model). Default is "2S". }
    \item{FDR}{False discovery rate. Default is 0.05. }    
    \item{maxgap}{Initial nearby peaks are merged if the distance (in bp) between them is less than \code{maxgap}. Default is 200. }     
    \item{minsize}{An initial peak is removed if its width is narrower than \code{minsize}. Default is 50. }
    \item{thres}{A bin within initial peak is removed if its ChIP tag counts are less than \code{thres}. Default is 10. }  
    \item{...}{ Other parameters to be passed through to generic \code{mosaicsPeak}.}
}
\details{
When peaks are called, proper signal model needs to be specified.
The optimal choice of the number of signal components depends on the characteristics of ChIP-seq data.
In order to support users in the choice of optimal signal model, 
Bayesian Information Criterion (BIC) values and Goodness of Fit (GOF) plot are provided.
BIC values and GOF plot can be obtained by applying \code{show} and \code{plot} methods
to the \code{MosaicsFit} class object, which is a fitted MOSAiCS model.
\code{maxgap}, \code{minsize}, and \code{thres} are for refining initial peaks called
using specified \code{signalModel} and \code{FDR}.

If you use a bin size shorter than the average fragment length of the experiment, 
set \code{maxgap} to the average fragment length and \code{minsize} to the bin size.
If you set the bin size to the average fragment length or if bin size is larger than the average fragment length,
set \code{maxgap} to the average fragment length and
\code{minsize} to a value smaller than the average fragment length. See the vignette for further details.
}
\value{
Construct \code{MosaicsPeak} class object.
}
\references{
Kuan, PF, D Chung, JA Thomson, R Stewart, and S Keles (2010), "A Statistical Framework
for the Analysis of ChIP-Seq Data", submitted (\url{http://works.bepress.com/sunduz_keles/19/}).
}
\author{ Dongjun Chung, Pei Fen Kuan, Sunduz Keles }
\seealso{
\code{\link{mosaicsFit}} , \code{\linkS4class{MosaicsPeak}}, \code{\linkS4class{MosaicsFit}}.
}
\examples{
\dontrun{
library(mosaicsExample)
data(exampleFit)

examplePeak <- mosaicsPeak( exampleFit, signalModel = "2S", FDR = 0.05 )
}
}
\keyword{models}
\keyword{methods}