\name{genomic_regions}
\Rdversion{1.1}
\alias{genomic_regions}
\alias{genomic_exons}
\alias{genomic_introns}
\title{
  (Deprecated) Functions that compute genomic regions of interest.
}
\description{
  Functions that compute genomic regions of interest such as promotor, 
  upstream regions etc, from the genomic locations provided in data like
  \code{geneMouse}.
  \strong{
    These functions are deprecated in favor of
    \code{\link[GenomicFeatures:regions]{transcripts}},
    \code{\link[GenomicFeatures:regions]{exons}}, and
    \code{\link[GenomicFeatures:regions]{introns}} in the \code{GenomicFeatures}
    package.
  }
}
\usage{
genomic_regions(genes, proximal = 500, distal = 10000)
genomic_exons(genes)
genomic_introns(genes)
}
\arguments{
  \item{genes}{ A data.frame like that provided by \code{geneMouse}.}
  \item{proximal}{
  The number of bases on either side of TSS and 3'-end for
  the promoter and end region, respectively.}
  \item{distal}{
The number of bases on either side for upstream/downstream,
i.e. enhancer/silencer regions.
}
}
\details{
Fairly simply additions/subtractions are made.
The assumption made for introns is that there must be more than one
exon, and that the introns are between the end of one exon and before
the start of the next exon.
}
\value{
For \code{genomic_regions} a data.frame with all components computed.
For \code{genomic_exons} a data.frame with one row per exon.
For \code{genomic_introns} a data.frame with one row per intron.
}
\author{
M. Lawrence.
}

\examples{
## use functions in GenomicFeatures
}