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Map between SomaScan SeqIds and gene names

SomaScanGENENAME.Rd

SomaScanGENENAME is an R object that maps SeqId to the corresponding gene name.

Details

Each SeqId maps to a named vector containing the gene name. The vector name corresponds to the SeqId. If the gene name is unknown, the vector will contain an NA.

Gene names currently include both the official (validated by a nomenclature committee) and preferred names (interim selected for display) for genes. Efforts are being made to differentiate the two by adding a name to the vector.

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:
x <- SomaScanGENENAME
# Get the probe identifiers that are mapped to a gene name
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0) {
    # Get the GENENAME for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "crystallin beta B2"