Map between SomaScan SeqIds and Mendelian Inheritance in Man (MIM) identifiers

SomaScanOMIM is an R object that provides mappings between manufacturer identifiers and OMIM identifiers.

Details

Each SeqIds is mapped to a vector of OMIM identifiers. The vector length may be one or longer, depending on how many OMIM identifiers the SeqIds maps to. An NA is reported for any SeqIds that cannot be mapped to an OMIM identifier at this time.

OMIM is based upon the book Mendelian Inheritance in Man (V. A. McKusick) and focuses primarily on inherited or heritable genetic diseases. It contains textual information, pictures, and reference information that can be searched using various terms, among which the MIM number is one.

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

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 <- SomaScanOMIM
# Get the probe identifiers that are mapped to a OMIM ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0) {
    # Get the OMIM for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "123620" "601547"