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Map between Common Gene Symbol Identifiers and SomaScan SeqIds

SomaScanALIAS2PROBE.Rd

SomaScanALIAS2PROBE is an R object that provides mappings between common gene symbol identifiers and manufacturer identifiers, i.e. the SomaScan SeqId.

Details

Each gene symbol is mapped to a named vector of SeqIds. The name of each vector element represents the gene symbol, and the vector contains all manufacturer identifiers that are found for that symbol. An NA is reported for any gene symbol that cannot be mapped to a SeqId.

This mapping includes all gene symbols, including those which are already listed in the SomaScanSYMBOL map. The SomaScanSYMBOL map is meant to only list official gene symbols, while the SomaScanALIAS maps are meant to store all used symbols.

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.

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:
# Convert the object to a list
xx <- as.list(SomaScanALIAS2PROBE)
if(length(xx) > 0){
    # Get the probe identifiers for the first two aliases
    xx[1:2]
    # Get the first value
    xx[[1]]
}
#> [1] "16561-9"  "9078-207"