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Get natural variants in UniProt by NIH-NCBI SNP database identifier

Source: R/uniprot_proteins.R
rba_uniprot_variation.Rd

Retrieve natural variant annotations of a sequence using UniProt protein accession, dbSNP or HGVS expression.

Usage

rba_uniprot_variation(
  id,
  id_type,
  source_type = NULL,
  consequence_type = NULL,
  wild_type = NULL,
  alternative_sequence = NULL,
  location = NULL,
  save_peff = FALSE,
  ...
)

Arguments

id

An ID which can be either a UniProt primary or secondary accession, NIH-NCBI dbSNP ID or HGVS expression. NIH-NCBI dbSNP id or HGVS Expression.

id_type

The type of supplied ID argument, one of: "uniprot", "dbsnp" or "hgvs"

source_type

Variation's source type. You can choose up to two of: "UniProt", "large scale study" and/or "mixed".

consequence_type

Variation's consequence type. You can choose up to two of: "missense", "stop gained" or "stop lost".

wild_type

Wild type amino acid. Accepted values are IUPAC single-letter amino acid (e.g. D for Aspartic acid) and "*" for stop codon. You can supply up to 20 values.

alternative_sequence

Alternative amino acid. Accepted values are IUPAC single-letter amino acid (e.g. D for Aspartic acid) and "*" for stop codon and "-" for deletion. You can supply up to 20 values.

location

A valid amino acid range (e.g. 10-25) within the sequence range where the variation occurs. You can supply up to 20 values.

save_peff

Logical or Character:

  • FALSE: (default) Do not save PEFF file, just return as a list object.

  • TRUE: Save as PEFF file to an automatically-generated path.

  • Character string: A valid file path to save the PEFF file.

...

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

Value

A list where each element is a list that corresponds to a UniProt protein entry.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/{dbid}"
"GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/{hgvs}"
"GET https://www.ebi.ac.uk/proteins/api/variation/{accession}"

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 - Variation": rba_uniprot_variation_search()

Examples

# \donttest{
rba_uniprot_variation(id = "rs121434451", id_type = "dbsnp")
# }
# \donttest{
rba_uniprot_variation(id = "NC_000008.11:g.22119227C>T", id_type = "hgvs")
# }
# \donttest{
rba_uniprot_variation(id = "O43593", id_type = "uniprot")
# }