\HeaderA{agREFSEQ}{Map between Manufacturer Identifiers and RefSeq Identifiers}{agREFSEQ}
\keyword{datasets}{agREFSEQ}
\begin{Description}\relax
agREFSEQ is an R environment that provides mappings between
manufacturer ids and RefSeq ids.
\end{Description}
\begin{Details}\relax
Each manufacturer id is mapped to a named vector of RefSeq ids. The
name represents the manufacturer id and the vector contains all RefSeq
ids that can be mapped to that manufacturer id. The length of the
vector may be one or greater, depending on how many RefSeq ids a given
manufacturer id can be mapped to. An \code{NA} is reported for any
manufacturer id that cannot be mapped to a RefSeq id at this time.

RefSeq ids differ in format according to the type of record the ids
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 ids.

Mappings were based on data provided by:

Entrez Gene:\url{http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/}. Built: Source data downloaded from Entrez Gene on Tue May 17 18:26:20 2005

Package built Tue May 17 18:29:49 2005
\end{Details}
\begin{References}\relax
\url{http://www.ncbi.nlm.nih.gov}
\url{http://www.ncbi.nlm.nih.gov/RefSeq/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert the environment to a list
    xx <- as.list(agREFSEQ)
    # Remove probe ids that do not map to any RefSeq
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
    # The RefSeq for the first two elements of XX
    xx[1:2]
    # Get the first one
    xx[[1]]
}
\end{ExampleCode}
\end{Examples}

