Use this function to search genomic coordinates of UniProt entries. You may also refine your search with modifiers such as chromosome, taxon id etc. See "Arguments section" for more information.

rba_uniprot_coordinates_search(
  accession = NULL,
  chromosome = NULL,
  ensembl_id = NULL,
  gene = NULL,
  protein = NULL,
  taxid = NULL,
  location = NULL,
  ...
)

Arguments

accession

UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

chromosome

chromosome name, such as "X", "Y", 1, 20, etc. You can supply up to 20 values.

ensembl_id

Ensembl Stable gene ID, transcript ID or translation ID. You can supply up to 20 IDs.

gene

UniProt gene name(s). You can supply up to 20 gene names.

protein

UniProt protein name

taxid

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

location

Genome location range such as "58205437-58219305"

...

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

Value

List where each element corresponds to one UniProt entity returned by your search query. The element itself is a sub-list containing that protein's coordinates information.

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.
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

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/coordinates"

References

  • 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

See also

Examples

# \donttest{
rba_uniprot_coordinates_search(taxid = 9606, chromosome = "y")
# }