Map Ensembl gene accession numbers with Entrez Gene identifiers

Description

org.Hs.egENSEMBL is an R object that contains mappings between Entrez Gene identifiers and Ensembl gene accession numbers.

Details

This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene to Ensembl gene Accession Numbers.

Mappings were based on data provided by BOTH of these sources: http://www.ensembl.org/biomart/martview/ ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

For most species, this mapping is a combination of NCBI to ensembl IDs from BOTH NCBI and ensembl. Users who wish to only use mappings from NCBI are encouraged to see the ncbi2ensembl table in the appropriate organism package. Users who wish to only use mappings from ensembl are encouraged to see the ensembl2ncbi table which is also found in the appropriate organism packages. These mappings are based upon the ensembl table which is contains data from BOTH of these sources in an effort to maximize the chances that you will find a match.

For worms and flies however, this mapping is based only on sources from ensembl, as these organisms do not have ensembl to entrez gene mapping data at NCBI.

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.egENSEMBL
# Get the entrez gene IDs that are mapped to an Ensembl ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the Ensembl gene IDs for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map ENSEMBL2EG:
# Convert to a list
xx <- as.list(org.Hs.egENSEMBL2EG)
if(length(xx) > 0){
   # Gets the entrez gene IDs for the first five Ensembl IDs
   xx[1:5]
   # Get the first one
   xx[[1]]
}