rbioapi (version 0.8.1)

rba_uniprot_coordinates: Get Genomic Coordinates of a Protein

Description

Using this function you can retrieve genomic Coordinates of a Protein by either providing the protein's UniProt accession or it's ID in a cross-reference database (Ensembl, CCDC, HGNC or RefSeq). You should supply either 'accession' alone or 'db_type' and 'db_id' together.

Usage

rba_uniprot_coordinates(accession = NULL, db_type = NULL, db_id = NULL, ...)

Value

A list with genome coordinates of your supplied protein.

Arguments

accession

UniProtKB primary or secondary accession.

db_type

cross-reference database name, Should be one of: "Ensembl", "CCDC", "HGNC" or "RefSeq".

db_id

Protein's ID in the cross-reference database

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/coordinates/{accession}"
"GET https://ebi.ac.uk/proteins/api/coordinates/{dbtype}:{dbid}"

Details

For more information about how UniProt imports and calculates genomic coordinates data, see:
McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J., Wu, C., & UniProt Consortium (2019). UniProt genomic mapping for deciphering functional effects of missense variants. Human mutation, 40(6), 694–705. https://doi.org/10.1002/humu.23738

References

• The UniProt Consortium, UniProt: the universal protein knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100

• Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237

• Proteins API Documentation

• Citations note on UniProt website

See Also

Other "UniProt - Coordinates": rba_uniprot_coordinates_location(), rba_uniprot_coordinates_search(), rba_uniprot_coordinates_sequence()

Examples

# \donttest{
rba_uniprot_coordinates(accession = "P25942")
# }
# \donttest{
rba_uniprot_coordinates(db_type = "HGNC", db_id = "CD40")
# }