Skip to contents

List matrices available in JASPAR of a species

Source: R/jaspar.R
rba_jaspar_species_matrices.Rd

JASPAR curates 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 species.

Usage

rba_jaspar_species_matrices(
  tax_id,
  release = 2022,
  only_last_version = FALSE,
  search = NULL,
  order = NULL,
  page_size = 1000,
  page = 1,
  ...
)

Arguments

tax_id

Numeric: NCBI taxonomic Identifier of species. Use rba_jaspar_species to get a list of supported Species.

release

Numeric: (default = 2022) Which JASPAR database release to use? Available options are: 2014, 2016, 2018, 2020, and 2022.

only_last_version

Logical: (default = FALSE) If TRUE, only the latest version of a matrix profile will be returned.

search

Character: A search term.

order

Character: A character string or a vector of character strings of field names that will be used to order the results.
Providing multiple field names is supported. You can also use prefix "-" before a field name to indicate reverse ordering.

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.

page

Numeric: Which page of the results to retrieve? The accepted values depend on the page size and number of results.

...

rbioapi option(s). See 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 species.

Details

The results are paginated. You can control the page's size number with the function's arguments. Also, you can use rba_pages to automatically iterate over multiple pages.

Corresponding API Resources

"GET "https://jaspar.genereg.net/api/v1/species/tax_id/"

References

  • Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, Anthony Mathelier, JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, https://doi.org/10.1093/nar/gkab1113

  • JASPAR API Documentation

  • Citations note on JASPAR website

See also

Other "JASPAR": rba_jaspar_collections_matrices(), rba_jaspar_collections(), rba_jaspar_matrix_search(), rba_jaspar_matrix_versions(), rba_jaspar_matrix(), rba_jaspar_releases(), rba_jaspar_sites(), rba_jaspar_species(), rba_jaspar_taxons_matrices(), rba_jaspar_taxons(), rba_jaspar_tffm_search(), rba_jaspar_tffm()

Examples

# \donttest{
rba_jaspar_species_matrices(tax_id = 9606, page_size = 100)
# }