Map between SomaScan SeqIds and Entrez gene identifiers

SomaScanENTREZID is an R object that provides mappings between SeqIds and Entrez Gene identifiers.

Details

Each SeqId is mapped to a vector of Entrez Gene identifiers. An NA is assigned to those SeqIds that can not be mapped to an Entrez Gene identifier at this time.

If a given SeqId can be mapped to different Entrez Gene identifiers from various sources, we attempt to select the common identifiers. If a concensus cannot be determined, we select the smallest identifier.

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: 2021-Sep13

Value

A Bimap object of the ProbeAnnDbBimap class.

References

https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

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 <- SomaScanENTREZID
# Get the probe identifiers that are mapped to an ENTREZ Gene ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0) {
    # Get the ENTREZID for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "1415"