Map between Entrez Gene Identifiers and RefSeq Identifiers

Description

org.Hs.egREFSEQ is an R object that provides mappings between entrez gene identifiers and RefSeq identifiers.

Details

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 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 https://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 With a date stamp from the source of: 2017-Nov6

References

https://www.ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/RefSeq/

See Also

• AnnotationDb-class for use of the 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 <- org.Hs.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.Hs.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]]
}