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Get a Position Frequency Matrices (PFM) with annotations

Source: R/jaspar.R
rba_jaspar_matrix.Rd

Using this function you can retrieve a Position Frequency Matrices (PFM) associated with a matrix profile Identifier along with its details and annotations. If a base ID (i.e. without version suffix) was supplied, the latest version will be returned.

Usage

rba_jaspar_matrix(matrix_id, file_format = NULL, save_to = NULL, ...)

Arguments

matrix_id

Character: A matrix profile Identifier. It has "base_id.version" naming schema.

file_format

Character: Instead of returning a R object, you can directly download the profile matrix in file with this format. Supported formats are: "yaml", "jaspar", "transfac", "meme" and "pfm"

save_to

NULL or Character:

  • NULL: (only if file_format was supplied) Save the file to an automatically-generated path.

  • Character string: A valid file or directory path to save the file to.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list that contains the PFM along with its details and annotations. If file_format was supplied, an un-parsed character string with the file's content.

Corresponding API Resources

"GET "https://jaspar.genereg.net/api/v1/matrix/matrix_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_releases(), rba_jaspar_sites(), rba_jaspar_species_matrices(), rba_jaspar_species(), rba_jaspar_taxons_matrices(), rba_jaspar_taxons(), rba_jaspar_tffm_search(), rba_jaspar_tffm()

Examples

# \donttest{
rba_jaspar_matrix("MA0600.2")
# }
if (FALSE) {
rba_jaspar_matrix(matrix_id = "MA0600.2",
                  file_format = "meme",
                  save_to = "my_matrix.meme")
}