rbioapi: rba_uniprot_proteomes_search – R documentation

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rba_uniprot_proteomes_search

Search Proteomes in UniProt

Description

UniProt collects and annotates proteomes (Protein sets expressed in an organism). Using this function you can search UniProt for available proteomes. see What are proteomes? for more information. You may also refine your search with modifiers such as keyword, taxon id etc. refer to "Arguments section" for more information.

Usage

rba_uniprot_proteomes_search(
  name = NA,
  upid = NA,
  taxid = NA,
  keyword = NA,
  xref = NA,
  genome_acc = NA,
  is_ref_proteome = NA,
  is_redundant = NA,
  ...
)

Arguments

`name`	a keyword in proteome's name
`upid`	UniProt Proteome identifier (UPID). You can provide up to 100 UPIDs.
`taxid`	NIH-NCBI Taxon ID. You can provide up to 20 taxon IDs.
`keyword`	Limit the search to entries that contain your provided keyword. see: UniProt Keywords
`xref`	Proteome cross-references such as Genome assembly ID or Biosample ID. You can provide up to 20 cross-reference IDs.
`genome_acc`	Genome accession associated with the proteome's components.
`is_ref_proteome`	(logical) If TRUE, only return reference proteomes; If FALSE, only returns non-reference proteomes; If NA (default), the results will not be filtered by this criteria see 'What are reference proteomes?' for more information.
`is_redundant`	(logical) If TRUE, only return redundant proteomes; If FALSE, only returns non-redundant proteomes; If NA (default), the results will not be filtered by redundancy. see 'Reducing proteome redundancy' for more information.
`...`	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

A list where each element is a list that corresponds to a single proteome (search hit) and contains informations pertinent to that proteome.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/proteomes"

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_proteomes_search(name = "SARS-CoV")


rba_uniprot_proteomes_search(name = "SARS-CoV", is_ref_proteome = TRUE)


rba_uniprot_proteomes_search(name = "SARS-CoV", is_ref_proteome = TRUE)


rba_uniprot_proteomes_search(genome_acc = "AY274119")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release