rbioapi: rba_uniprot_coordinates_location – R documentation

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rba_uniprot_coordinates_location

Search UniProt entries by taxonomy and genomic coordinates

Description

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

Usage

rba_uniprot_coordinates_location(
  taxid,
  locations,
  in_range = TRUE,
  feature = FALSE,
  ...
)

Arguments

`taxid`	NIH-NCBI Taxon ID.
`locations`	genomic location formatted as: chromosome:start-end. (e.g. "Y:17100001-19600000"). If you omit chromosome, it will be interpreted as any chromosome (e.g. "1-10000").
`in_range`	Only return proteins that are in range.
`feature`	(logical) Get features?
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

Value

a list containing UniProt proteins which match the provided genomic location and taxonomy ID.

Corresponding API Resources

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

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_location(taxid = 9606,
    locations = "Y:17100001-19600000", in_range = TRUE)


rba_uniprot_coordinates_location(taxid = 9606,
    locations = "20:39000001", in_range = FALSE)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release