Skip to content

Map between SomaScan SeqIds and RefSeq identifiers

SomaScanREFSEQ.Rd

SomaScanREFSEQ is an R object that provides mappings between SeqIds and RefSeq identifiers.

Details

Each manufacturer identifier is mapped to a named vector of RefSeq identifiers. The name represents the manufacturer identifier, and the vector contains all RefSeq identifiers that can be mapped to that SeqId. The length of the vector may be one or greater, depending on how many RefSeq identifiers a given SeqId can be mapped to. An NA is reported for any SeqId that cannot be mapped to a RefSeq identifier at this time.

RefSeq identifiers differ in format according to the type of record. See the identifier descriptions below, where XXXXX is a sequence of integers:

  • NG_XXXXX: RefSeq accessions for genomic region (nucleotide) records

  • NM_XXXXX: RefSeq accessions for mRNA records

  • NC_XXXXX: RefSeq accessions for chromosome records

  • NP_XXXXX: RefSeq accessions for protein records

  • XR_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products

  • XM_XXXXX: RefSeq accessions for model mRNA records

  • XP_XXXXX: RefSeq accessions for model protein records

NCBI (https://www.ncbi.nlm.nih.gov/RefSeq/) allows users to query the RefSeq database using RefSeq identifiers.

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 https://www.ncbi.nlm.nih.gov/RefSeq/

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 <- SomaScanREFSEQ
# Get the probe identifiers that are mapped to any RefSeq ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes][1:300])
if(length(xx) > 0) {
    # Get the REFSEQ for the first five probes
    xx[1:5]
    # Get the first value
    xx[[1]]
}
#> [1] "NM_000496"    "NP_000487"    "XM_006724141" "XM_054325114"
#> [5] "XM_054325115" "XP_006724204" "XP_054181089" "XP_054181090"