\name{@ANNOBJPREFIX@REFSEQ}
\alias{@ANNOBJPREFIX@REFSEQ}
\alias{@ANNOBJPREFIX@REFSEQ2TAIR}
\title{Map between TAIR Identifiers and RefSeq Identifiers}
\description{
   @ANNOBJPREFIX@REFSEQ is an R object that provides mappings between
   TAIR identifiers and RefSeq identifiers.
}
\details{
  Each TAIR identifier is mapped to a named vector of RefSeq
  identifiers. The name represents the TAIR identifier and the vector
  contains all RefSeq identifiers that can be mapped to that TAIR
  identifier. The length of the vector may be one or greater, depending
  on how many RefSeq identifiers a given TAIR identifier can be mapped
  to. An \code{NA} is reported for any TAIR identifier that cannot be
  mapped to a RefSeq identifier at this time.

  RefSeq identifiers differ in format according to the type of record
  the identifiers are for as shown below:

  NG\_XXXXX: RefSeq accessions for genomic region (nucleotide) records

  NM\_XXXXX: RefSeq accessions for mRNA records

  NC\_XXXXX: RefSeq accessions for chromosome records

  NP\_XXXXX: RefSeq accessions for protein records

  XR\_XXXXX: RefSeq accessions for model RNAs that are not associated with
  protein products

  XM\_XXXXX: RefSeq accessions for model mRNA records

  XP\_XXXXX: RefSeq accessions for model protein records

  Where XXXXX is a sequence of integers.

  NCBI \url{http://www.ncbi.nlm.nih.gov/RefSeq/} allows users to query
  the RefSeq database using RefSeq identifiers.

  Mappings were based on data provided by:
  \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA}

}

\references{
    \url{http://www.ncbi.nlm.nih.gov}
    \url{http://www.ncbi.nlm.nih.gov/RefSeq/} 
}

\seealso{
  \itemize{
    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
          the \code{select()} interface.
  }
}

\examples{
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- @ANNOBJPREFIX@REFSEQ
# Get the TAIR identifiers that are mapped to any RefSeq ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the REFSEQ for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}

# For the reverse map:
x <- @ANNOBJPREFIX@REFSEQ2TAIR
# Get the RefSeq identifier that are mapped to an TAIR ID
mapped_seqs <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_seqs])
if(length(xx) > 0) {
  # Get the TAIR ID for the first five Refseqs
  xx[1:5]
  # Get the first one
  xx[[1]]
}
}

\keyword{datasets}

