rbioapi: rba_uniprot_coordinates_search – R documentation

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rba_uniprot_coordinates_search

Search Genomic Coordinates of UniProt entries

Description

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

Usage

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

Arguments

`accession`	UniProtKB primary or secondary accession(s). You can provide up to 100 accession numbers.
`chromosome`	chromosome name, such as "X", "Y", 1, 20, etc. You can provide up to 20 values.
`ensembl_id`	Ensembl Stable gene ID, transcript ID or translation ID. You can provide up to 20 IDs.
`gene`	UniProt gene name(s). You can provide up to 20 gene names.
`protein`	UniProt protein name
`taxid`	NIH-NCBI Taxon ID. You can provide up to 20 taxon IDs.
`location`	Genome location range such as "58205437-58219305"
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

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

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.

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

Examples

rba_uniprot_coordinates_search(taxid = 9606, chromosome = "y")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release