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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, ...)

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.

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.

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

Examples

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