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rba_uniprot_coordinates_search.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/uniprot_coordinates.R
\name{rba_uniprot_coordinates_search}
\alias{rba_uniprot_coordinates_search}
\title{Search Genomic Coordinates of UniProt entries}
\usage{
rba_uniprot_coordinates_search(
accession = NULL,
chromosome = NULL,
ensembl_id = NULL,
gene = NULL,
protein = NULL,
taxid = NULL,
location = 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{chromosome}{chromosome name, such as "X", "Y", 1, 20, etc. You can
supply up to 20 values.}
\item{ensembl_id}{Ensembl Stable gene ID, transcript ID or translation ID.
You can supply up to 20 IDs.}
\item{gene}{\href{https://www.uniprot.org/help/gene_name}{UniProt gene
name(s)}. You can supply up to 20 gene names.}
\item{protein}{\href{https://www.uniprot.org/help/protein_names}{UniProt
protein name}}
\item{taxid}{NIH-NCBI \href{https://www.uniprot.org/taxonomy/}{Taxon ID}.
You can supply up to 20 taxon IDs.}
\item{location}{Genome location range such as "58205437-58219305"}
\item{...}{rbioapi option(s). See \code{\link{rba_options}}'s
arguments manual for more information on available options.}
}
\value{
List where each element corresponds to one UniProt entity returned
by your search query. The element itself is a sub-list containing that
protein's coordinates information.
}
\description{
Use this function to search genomic coordinates of UniProt entries.
You may also refine your search with modifiers such as chromosome, taxon
id 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 For more information about how UniProt imports and calculates genomic
coordinates data, see:
\cr McGarvey, P. B., Nightingale, A., Luo, J., Huang, H., Martin, M. J.,
Wu, C., & UniProt Consortium (2019). UniProt genomic mapping for
deciphering functional effects of missense variants. Human mutation,
40(6), 694–705. https://doi.org/10.1002/humu.23738
}
\section{Corresponding API Resources}{
"GET https://ebi.ac.uk/proteins/api/coordinates"
}
\examples{
\donttest{
rba_uniprot_coordinates_search(taxid = 9606, chromosome = "y")
}
}
\references{
\itemize{
\item The UniProt Consortium , UniProt: the Universal Protein
Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010,
https://doi.org/10.1093/nar/gkae1010
\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 - Coordinates":
\code{\link{rba_uniprot_coordinates}()},
\code{\link{rba_uniprot_coordinates_location}()},
\code{\link{rba_uniprot_coordinates_location_genome}()},
\code{\link{rba_uniprot_coordinates_location_protein}()}
}
\concept{"UniProt - Coordinates"}