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rba_jaspar_taxons_matrices.Rd
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rba_jaspar_taxons_matrices.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jaspar.R
\name{rba_jaspar_taxons_matrices}
\alias{rba_jaspar_taxons_matrices}
\title{List matrices available in JASPAR of a taxonomic group}
\usage{
rba_jaspar_taxons_matrices(
tax_group,
release = 2024,
only_last_version = FALSE,
search = NULL,
order = NULL,
page_size = 1000,
page = 1,
...
)
}
\arguments{
\item{tax_group}{Character: Taxonomic group. Use
\code{\link{rba_jaspar_taxons}} to get a list of supported Taxonomic
groups.}
\item{release}{Numeric: (default = 2024) Which JASPAR database release
to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.}
\item{only_last_version}{Logical: (default = FALSE) If TRUE, only the
latest version of a matrix profile will be returned.}
\item{search}{Character: A search term.}
\item{order}{Character: A character string or a vector of character strings
of field names that will be used to order the results.
\cr Providing multiple field names is supported. You can also use prefix
"-" before a field name to indicate reverse ordering.}
\item{page_size}{Numeric: (default = 1000) This resource returns paginated
results. What is the maximum numbers of results that you want to retrieve
per a page? Accepted values are between 1 and 1000.}
\item{page}{Numeric: Which page of the results to retrieve? The accepted
values depend on the page size and number of results.}
\item{...}{rbioapi option(s). See \code{\link{rba_options}}'s
arguments manual for more information on available options.}
}
\value{
A list that contains a data frame with information of matrix
profiles available for the taxonomic group.
}
\description{
JASPAR organizes matrix profiles from multiple species
in six taxonomic groups. Using this function you can list all
matrix profiles that are available in a JASPAR release from a
taxonomic group.
}
\details{
The results are paginated. You can control the page's size number
with the function's arguments. Also, you can use \code{\link{rba_pages}}
to automatically iterate over multiple pages.
}
\section{Corresponding API Resources}{
"GET https://jaspar.elixir.no/api/v1/taxon/\{tax_group\}/"
}
\examples{
\donttest{
rba_jaspar_taxons_matrices(tax_group = "plants", page_size = 100)
}
}
\references{
\itemize{
\item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R,
Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J,
Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard
B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024:
20th anniversary of the open-access database of transcription factor
binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059
\item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data
from any programming language. Bioinformatics, 2017,
doi: 10.1093/bioinformatics/btx804
\item
\href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation}
\item \href{https://jaspar.elixir.no/faq/}{Citations note
on JASPAR website}
}
}
\seealso{
Other "JASPAR":
\code{\link{rba_jaspar_collections}()},
\code{\link{rba_jaspar_collections_matrices}()},
\code{\link{rba_jaspar_matrix}()},
\code{\link{rba_jaspar_matrix_search}()},
\code{\link{rba_jaspar_matrix_versions}()},
\code{\link{rba_jaspar_releases}()},
\code{\link{rba_jaspar_sites}()},
\code{\link{rba_jaspar_species}()},
\code{\link{rba_jaspar_species_matrices}()},
\code{\link{rba_jaspar_taxons}()},
\code{\link{rba_jaspar_tffm}()},
\code{\link{rba_jaspar_tffm_search}()}
}
\concept{"JASPAR"}