Get proteome by proteome/proteins UPID
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.
rba_uniprot_proteomes(upid, get_proteins = FALSE, reviewed = NA, ...)
upid |
UniProt Proteome identifier (UPID). You can provide up to 100 UPIDs. |
get_proteins |
logical: set FALSE (default) to only return information of the proteome with provided UPID, set TRUE to also return the proteins of the provided 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 NA if you do not want to filter proteins based on their review status. |
... |
rbioapi option(s). Refer to |
a list containing information of the proteome with your provided UPID that can contain the proteomes protein entries based on the value of get_proteins argument.
"GET https://ebi.ac.uk/proteins/api/proteomes/proteins/upid"
"GET https://ebi.ac.uk/proteins/api/proteomes/upid"
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
Other "UniProt - Proteomes":
rba_uniprot_genecentric_search(),
rba_uniprot_genecentric(),
rba_uniprot_proteomes_search()
rba_uniprot_proteomes(upid = "UP000000354") rba_uniprot_proteomes(upid = "UP000000354", get_proteins = TRUE)
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