rbioapi: rba_uniprot_variation_search – R documentation

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rba_uniprot_variation_search

Search UniProt Natural Variants

Description

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. refer to "Arguments section" for more information.

Usage

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

Arguments

`accession`	UniProtKB primary or secondary accession(s). You can provide 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 provide 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 provide up to 20 values.
`location`	A valid amino acid range (e.g. 10-25) within the sequence range where the variation occurs. You can provide 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 provide up to 20 values.
`omim`	OMIM ID that is associated with a variation. You can provide up to 20 values.
`evidence`	Pubmed ID of the variation's citation You can provide up to 20 values.
`taxid`	NIH-NCBI Taxon ID. You can provide up to 20 taxon IDs.
`db_type`	cross-reference database of the variation. You can provide up to two of the following: "dbSNP": NIH-NCBI dbSNP database. "cosmic curate": COSMIC (the Catalogue of Somatic Mutations in Cancer) "ClinVar": NIH-NCBI ClinVar
`db_id`	The variation ID in a Cross-reference (external) database. You can provide 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). 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.

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.

Corresponding API Resources

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

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_variation_search(accession = "P05067")


rba_uniprot_variation_search(disease = "alzheimer disease, 18")


rba_uniprot_variation_search(disease = "alzheimer",
    wild_type = "A", alternative_sequence = "T")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release