rbioapi: rba_uniprot_proteomics_search – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

rba_uniprot_proteomics_search

Search Proteomics Peptides in UniProt

Description

UniProt maps proteomics peptides from different sources to the proteins' sequences. Using this function, you can search for proteomics peptides that has been map to UniProt proteins. You may also refine your search with modifiers such as data_source, peptide etc. refer to "Arguments section" for more information.

Usage

rba_uniprot_proteomics_search(
  accession = NA,
  data_source = NA,
  taxid = NA,
  upid = NA,
  peptide = NA,
  unique = NA,
  ...
)

Arguments

`accession`	UniProtKB primary or secondary accession(s). You can provide up to 100 accession numbers.
`data_source`	Proteomics data source. You can choose up to two of: "MaxQB" "PeptideAtlas" "EPD" "ProteomicsDB"
`taxid`	NIH-NCBI Taxon ID. You can provide up to 20 taxon IDs.
`upid`	UniProt Proteome identifier (UPID). You can provide up to 100 UPIDs.
`peptide`	Peptide sequence(s). You can provide up to 20 sequences.
`unique`	Logical: Should the results be filtered based on the Peptide's uniqueness (the fact that a peptide maps to only 1 protein). If TRUE, Only unique peptides will be returned, if FALSE only un-unique peptides will be returned; If NA (default) the results will not be filtered based on this.
`...`	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.
see also: Mass spectrometry-based proteomics data in UniProtKB

Value

A list Where each element correspond to a UniProt protein and proteomics peptides are organized under the "features" sub-list.

Corresponding API Resources

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

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_proteomics_search(peptide = "MEDYTKIEK")


rba_uniprot_proteomics_search(peptide = "MEDYTKIEK")

## Not run: 
### this will generate a very large response!
  rba_uniprot_proteomics_search(taxid = 9606,
  data_source = "PeptideAtlas",
  progress = TRUE, timeout = 999999, unique = TRUE)

## End(Not run)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release