\HeaderA{org.EcK12.egREFSEQ}{Map between Entrez Gene Identifiers and RefSeq Identifiers}{org.EcK12.egREFSEQ}
\aliasA{org.EcK12.egREFSEQ2EG}{org.EcK12.egREFSEQ}{org.EcK12.egREFSEQ2EG}
\keyword{datasets}{org.EcK12.egREFSEQ}
\begin{Description}\relax
org.EcK12.egREFSEQ is an R object that provides mappings between
entrez gene identifiers and RefSeq identifiers.
\end{Description}
\begin{Details}\relax
Each entrez gene identifier is mapped to a named vector of RefSeq
identifiers. The name represents the entrez gene identifier and the
vector contains all RefSeq identifiers that can be mapped to that
entrez gene identifier. The length of the vector may be one or
greater, depending on how many RefSeq identifiers a given entrez gene
identifier can be mapped to. An \code{NA} is reported for any entrex
gene 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: Entrez Gene ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2008-Sep2
\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}
        x <- org.EcK12.egREFSEQ
        # Get the entrez gene 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 <- org.EcK12.egREFSEQ2EG
        # Get the RefSeq identifier that are mapped to an entrez gene ID
        mapped_seqs <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_seqs])
        if(length(xx) > 0) {
          # Get the entrez gene for the first five Refseqs
          xx[1:5]
          # Get the first one
          xx[[1]]
        }
\end{ExampleCode}
\end{Examples}

