\name{easyRNASeq annotation internal methods}

\alias{.getBmRange}
\alias{.getGffRange}
\alias{.getGtfRange}
\alias{.geneModelAnnotation}
\alias{.readGffGtf}

\title{Internal easyRNASeq annotation methods}

\description{
	These are internal methods used to retrieve annotations
	tabular{ll}{
		\code{.getBmRange}{Use \code{\link[biomaRt:useMart]{biomaRt}} to get exon annotations.}
		\code{.getGffRange}{Use \code{\linkS4class{Genome_intervals_stranded}} to get annotation from a gff file.}
		\code{.getGtfRange}{Use \code{\linkS4class{Genome_intervals_stranded}} to get annotation from a gtf file.}
		\code{.geneModelAnnotation}{Use the provided exon annotation to define gene models.}
		\code{.readGffGtf}{Use \code{\linkS4class{Genome_intervals_stranded}} to get annotation from a gff or gtf file. It is called from \code{getGffRange}{} and	\code{getGtfRange}.}
	}
}

\usage{
	.getBmRange(organism=character(1),...)
	.getGffRange(organism=character(1),filename=filename,ignoreWarnings = FALSE,...)
	.getGtfRange(organism=character(1),filename=filename,ignoreWarnings = FALSE,...)
	.geneModelAnnotation(gAnnot,nbCore=1)
	.readGffGtf(filename=filename,annotation.type=c("exon"),ignoreWarnings = FALSE,...)
}

\arguments{
	\item{annotation.type}{describes the kind of annotation to keep the information from in a gtf or gff file. If set to NULL all the annotations are returned.}  
	\item{organism}{Organism name}
	\item{gAnnot}{a \code{\linkS4class{RangedData}} object containing exon annotations}
	\item{nbCore}{number of CPU cores to use}
	\item{filename}{filename that contains the annotations}
	\item{\dots}{Additional arguments, passed to more internal functions.} 
}


\value{
	A \code{\linkS4class{RangedData}} containing the loaded or processed annotations.
}

\details{
  To use multicore machines more efficiently, the default parallel package will be used to parallelize the processing.
}

\author{Nicolas Delhomme}

\keyword{internal}