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Search UniProt Natural Variants

Source: R/uniprot_proteins.R
rba_uniprot_variation_search.Rd

Using this function, you can search and retrieve Natural variant(s) that has been annotated in the protein's sequences. You may also refine your search with modifiers such as source type, disease etc. See "Arguments section" for more information.

Usage

rba_uniprot_variation_search(
  accession = NULL,
  source_type = NULL,
  consequence_type = NULL,
  wild_type = NULL,
  alternative_sequence = NULL,
  location = NULL,
  disease = NULL,
  omim = NULL,
  evidence = NULL,
  taxid = NULL,
  db_type = NULL,
  db_id = NULL,
  save_peff = FALSE,
  ...
)

Arguments

accession

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

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.

disease

Human disease that are associated with a sequence variation. Accepted values are disease name (e.g. Alzheimer disease 18), partial disease name (Alzheimer) and/or disease acronym (e.g. AD). You can supply up to 20 values.

omim

OMIM ID that is associated with a variation. You can supply up to 20 values.

evidence

Pubmed ID of the variation's citation You can supply up to 20 values.

taxid

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

db_type

cross-reference database of the variation. You can supply up to two of the following:

db_id

The variation ID in a Cross-reference (external) database. 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

List where each element corresponds to one UniProt entity returned by your search query. The element itself is a sub-list containing all information that UniProt has about that Variation.

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.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/variation"

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()

Examples

# \donttest{
rba_uniprot_variation_search(accession = "P05067")
# }
# \donttest{
rba_uniprot_variation_search(disease = "alzheimer disease, 18")
# }
# \donttest{
rba_uniprot_variation_search(disease = "alzheimer",
    wild_type = "A", alternative_sequence = "T")
# }