rbioapi (version 0.8.1)

rba_uniprot_proteomes: Get proteome by proteome/proteins UPID

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.

Usage

rba_uniprot_proteomes(upid, get_proteins = FALSE, reviewed = NULL, ...)

Value

a list containing information of the proteome with your supplied UPID that can contain the proteomes protein entries based on the value of get_proteins argument.

Arguments

upid

UniProt Proteome identifier (UPID). You can supply up to 100 UPIDs.

get_proteins

logical: set FALSE (default) to only return information of the proteome with supplied UPID, set TRUE to also return the proteins of the supplied proteome UPID.

reviewed

Logical: Only considered when get_proteins is TRUE. If TRUE, only return "UniProtKB/Swiss-Prot" (reviewed) proteins; If FALSE, only return TrEMBL (un-reviewed) entries. leave it as NULL if you do not want to filter proteins based on their review status.

...

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

Corresponding API Resources

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

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 - Proteomes": rba_uniprot_genecentric(), rba_uniprot_genecentric_search(), rba_uniprot_proteomes_search()

Examples

# \donttest{
rba_uniprot_proteomes(upid = "UP000000354")
# }
# \donttest{
rba_uniprot_proteomes(upid = "UP000000354", get_proteins = TRUE)
# }