\name{easyRNASeq de-novo annotation methods}
\alias{findIslands}

\title{Identify expressed regions de-novo}

\description{
	Process the coverage to locate regions with a minimum coverage (min.cov). If regions are separated by a gap 
	shorter than a maximum length (max.gap), they are unified. Only islands longer than min.length are returned.
	These functions are now outdated and would need to be actualized.
}

\usage{
  findIslands(obj,max.gap=integer(1),min.cov=1L,min.length=integer(1),plot=TRUE,...) 
}

\arguments{
  \item{obj}{An object of class \code{RNAseq}}
  \item{max.gap}{Maximum gap between two peaks to build an island}
  \item{min.cov}{Minimum coverage for an island to be returned}
  \item{min.length}{Minimum size of an island to be returned}
  \item{plot}{If TRUE, draw plots of coverage distribution. Help the user to select an appropriate value for the minimum coverage.}
  \item{\dots}{See details}
}

\details{
	\dots are for providing additional options to the \code{\link[graphics:hist]{hist}} plot function.
}

\value{
	An \code{RNAseq} object with the readIsland slot set with a RangedData containing the selected islands and 
	the readCount slot actualized with a list containing the count table per island.
}

\examples{
	\dontrun{
	## NOTE that this function might need to be actualized
	obj <- new('RNAseq',
		organismName="Dmelanogaster",
		readLength=36L,
		chrSize=as.list(seqlengths(Dmelanogaster))
		)

	obj <- fetchCoverage(
			obj,
			format="bam",
                        filename=system.file(
				"extdata",
				"ACACTG.bam",
                            	package="RnaSeqTutorial")
			)

	obj <- findIslands(
			obj,
			max.gap=10L,
			min.cov=10L,
			min.length=200L)
	}
}

\author{Nicolas Delhomme}
\keyword{connection}
\keyword{data}
\keyword{methods}