Map Ensembl gene accession numbers with Entrez Gene identifiers

SomaScanENSEMBL is an R object that contains mappings between SeqIds and Ensembl gene accession numbers.

Details

This object is a simple mapping of SeqIds to Ensembl gene accession numbers.

For most species, this mapping is a combination of SeqIds 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, like ncbi2ensembl, is found in the appropriate organism package. These mappings are based upon the Ensembl table, which contains data from both of these sources in an effort to maximize the chances of finding a match.

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

Value

A Bimap object of the ProbeAnnDbBimap class.

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 <- SomaScanENSEMBL
# 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][1:300])
if(length(xx) > 0) {
    # Get the Ensembl gene IDs for the first five genes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "ENSG00000244752"

# For the reverse map ENSEMBL2PROBE:
x <- SomaScanENSEMBL2PROBE
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes][1:300])
if(length(xx) > 0){
    # Gets the entrez gene IDs for the first five Ensembl IDs
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "10000-28"