rbioapi: rba_uniprot_coordinates_sequence – R documentation

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rba_uniprot_coordinates_sequence

Get Genome coordinate by Protein Sequence position

Description

Using this function you can retrieve genome coordinates of a given UniProt protein by providing protein position or position range. You can either provide 'p_position' alone or provide 'p_start' and 'p_end' together.

Usage

rba_uniprot_coordinates_sequence(
  accession,
  p_position = NA,
  p_start = NA,
  p_end = NA,
  ...
)

Arguments

`accession`	UniProtKB primary or secondary accession.
`p_position`	(numeric) Protein sequence position
`p_start`	(numeric) Protein sequence position start
`p_end`	(numeric) Protein sequence position end
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

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

Value

Genome coordinates of your provided proteins.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/coordinates/location/accession:pPosition"
"GET https://ebi.ac.uk/proteins/api/coordinates/location/accession:pStart-pEnd"

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_sequence(accession = "P25942", p_position = 1)


rba_uniprot_coordinates_sequence(accession = "P25942",
    p_start = 1, p_end = 277)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release