\name{DESeq edgeR common methods}

\alias{plotDispersionEstimates}
\alias{plotDispersionEstimates,CountDataSet-method}
\alias{plotDispersionEstimates,DGEList-method}

\title{DESeq and edgeR common methods}

\description{
	\code{plotDispersionEstimates(obj,...)} extends the \pkg{DESeq} and \pkg{edgeR} packages by offering the functionality to plot the dispersion estimate as described in their respective vignettes: \code{\linkS4class{CountDataSet}{DESeq}} and \code{\link[edgeR:edgeR-package]{edgeR}}.
}

\usage{
	plotDispersionEstimates(obj,...)
}

\arguments{
  \item{obj}{An object of class \code{\linkS4class{CountDataSet}} or of class \code{\linkS4class{DGEList}}}
  \item{\dots}{See details}
}

\details{
	\itemize{
	\item{\code{\linkS4class{CountDataSet}{DESeq}}} A character string describing the first condition, to be provided as cond=value
	\item{\code{\link[edgeR:edgeR-package]{edgeR}}} Unused, just for compatibility.
	}
}

\value{
	none
}

\examples{
	\dontrun{
	## edgeR
	## create the object
	dgeList <- DGEList(counts,group)
	## calculate the sie factors
	dgeList <- calcNormFactors(dgeList)
	## plot them
	apply(combn(rownames(dgeList$samples),2),
		2,
		function(co,obj){plotNormalizationFactors(obj,co[1],co[2])},dgeList)
	## the dispersion estimates
	plotDispersionEstimates(obj)
	
	## DESeq
	## these are helper function for the DESeq package
	## refer to its vignette first
	cds <- newCountDataSet(countData,conditions)
	cds <- estimateSizeFactors(cds)
	cds <- estimateDispersions(cds)
	plotDispersionEstimates(cds,conditions[1])
	}
}

\author{Nicolas Delhomme}

\keyword{methods}