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rba_uniprot_proteomics_search.Rd
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rba_uniprot_proteomics_search.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/uniprot_proteins.R
\name{rba_uniprot_proteomics_search}
\alias{rba_uniprot_proteomics_search}
\title{Search Proteomics Peptides in UniProt}
\usage{
rba_uniprot_proteomics_search(
accession = NULL,
data_source = NULL,
taxid = NULL,
upid = NULL,
peptide = NULL,
unique = NULL,
...
)
}
\arguments{
\item{accession}{\href{https://www.uniprot.org/help/accession_numbers}{
UniProtKB primary or secondary accession}(s). You can supply up to 100
accession numbers.}
\item{data_source}{Proteomics data source. You can choose up to two of:
\itemize{
\item \href{https://www.uniprot.org/database/DB-0186}{"MaxQB"}
\item \href{https://www.uniprot.org/database/DB-0071}{"PeptideAtlas"}
\item \href{https://www.uniprot.org/database/DB-0205}{"EPD"}
\item \href{https://www.uniprot.org/database/DB-0229}{"ProteomicsDB"}
}}
\item{taxid}{NIH-NCBI \href{https://www.uniprot.org/taxonomy/}{Taxon ID}.
You can supply up to 20 taxon IDs.}
\item{upid}{\href{https://www.uniprot.org/help/proteome_id}{UniProt Proteome
identifier (UPID)}. You can supply up to 100 UPIDs.}
\item{peptide}{Peptide sequence(s). You can supply up to 20 sequences.}
\item{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 NULL (default) the results will not be
filtered based on this.}
\item{...}{rbioapi option(s). See \code{\link{rba_options}}'s
arguments manual for more information on available options.}
}
\value{
A list Where each element correspond to a UniProt protein and
proteomics peptides are organized under the "features" sub-list.
}
\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. See
"Arguments section" for more information.
}
\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.
\cr see also: \href{https://www.uniprot.org/help/proteomics}{Mass
spectrometry-based proteomics data in UniProtKB}
}
\section{Corresponding API Resources}{
"GET https://www.ebi.ac.uk/proteins/api/proteomics"
}
\examples{
\donttest{
rba_uniprot_proteomics_search(peptide = "MEDYTKIEK")
}
\donttest{
rba_uniprot_proteomics_search(peptide = "MEDYTKIEK")
}
\dontrun{
### this will generate a very large response!
rba_uniprot_proteomics_search(taxid = 9606,
data_source = "PeptideAtlas",
progress = TRUE, timeout = 999999, unique = TRUE)
}
}
\references{
\itemize{
\item 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
\item 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
\item \href{https://www.ebi.ac.uk/proteins/api/doc/}{Proteins API
Documentation}
\item \href{https://www.uniprot.org/help/publications}{Citations note
on UniProt website}
}
}
\seealso{
Other "UniProt - Proteomics":
\code{\link{rba_uniprot_proteomics}()}
}
\concept{"UniProt - Proteomics"}