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Map between SomaScan SeqIds and Gene Symbols

SomaScanSYMBOL.Rd

SomaScanSYMBOL is an R object that provides mappings between SeqIds and gene abbreviations.

Details

Each SeqId is mapped to an abbreviation (symbol) for the corresponding gene. An NA is reported if there is no known abbreviation for a given gene.

Symbols typically consist of 3-6 letters that define either a single gene (ABC) or multiple genes (ABC1, ABC2, ABC3). Gene symbols can be used as key words to query public databases such as Entrez Gene.

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 <- SomaScanSYMBOL
# Get the probe identifiers that are mapped to a gene symbol
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0) {
    # Get the SYMBOL for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "CRYBB2"