\name{easyRNASeq correction methods}

\alias{RPKM}
\alias{RPKM,RNAseq,ANY,ANY,ANY-method}
\alias{RPKM,matrix,ANY,vector,vector-method}

\title{easyRNASeq count table correction to RPKM}

\description{
	Convert a count table obtained from the easyRNASeq function into an RPKM corrected count table.
}

\usage{
	RPKM(obj,
	from=c("exons","features","transcripts","bestExons","geneModels","islands"),
	lib.size=numeric(1),
	feature.size=numeric(1),
	unique=TRUE,...)
}

\arguments{
  \item{feature.size}{Precise the feature (e.g. exons, genes) sizes. It should be a named numeric list, named after the feature names.} 
  \item{from}{Determine the kind of coverage to use, choice limited to: exons, features, transcripts, bestExons, geneModels or islands.}
  \item{lib.size}{Precise the library size. It should be a named numeric list, i.e. named after the sample names.}
  \item{obj}{An object of class \code{\linkS4class{RNAseq}} or a \code{matrix}, see details}
  \item{unique}{If set to TRUE, whenever a feature (exon, feature, ...) is duplicated in the count table, it is only returned once.}
  \item{\dots}{additional arguments. See details}
}

\value{
	A \code{matrix} containing RPKM corrected read counts.
}

\details{
	RPKM accepts two sets of arguments:
	\itemize{
	\item{RNAseq,character} the \dots are additional arguments to be passed to the \code{\link[easyRNASeq:easyRNASeq-accessors]{readCounts}} method.
	\item{matrix,named vector} normalize a count matrix by providing the feature sizes (e.g. gene sizes) as a named vector where the names match the row names of the count matrix and the lib sizes as a named vector where the names match the column names of the count matrix .
	}
}

\examples{

	\dontrun{
	## get an RNAseq object
	rnaSeq <- easyRNASeq(filesDirectory=
		    			system.file(
					"extdata",
					package="RnaSeqTutorial"),
					pattern="[A,C,T,G]{6}\\.bam$",
				format="bam",
				readLength=36L,
				organism="Dmelanogaster",
				chr.sizes=as.list(seqlengths(Dmelanogaster)),
				annotationMethod="rda",
				annotationFile=system.file(
				                            "data",
							    "gAnnot.rda",
							    package="RnaSeqTutorial"),
				count="exons",
				outputFormat="RNAseq")

	## get the RPKM
	rpkm <- RPKM(rnaSeq,from="exons")
	
	## the same from a count table
	count.table <- readCounts(rnaSeq,count="exons")

	## get the RPKM
	## verify that the feature are sorted as the count.table
	all(.getName(rnaSeq,"exon") == rownames(count.table))
	feature.size <- unlist(width(ranges(rnaSeq)))

	## verify that the samples are ordered in the same way
	all(names(librarySize(rnaSeq)) == colnames(count.table))

	## get the RPKM
	rpkm <- RPKM(count.table,
			feature.size=feature.size,
			lib.size=librarySize(rnaSeq))
}
}

\seealso{
	\code{\link[easyRNASeq:easyRNASeq-accessors]{readCounts}}
}

\author{Nicolas Delhomme}

\keyword{methods}