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Get a position frequency matrix (PFM) with annotations

Source: R/jaspar.R
rba_jaspar_matrix.Rd

Using this function, you can retrieve the position frequency matrix (PFM) associated with a matrix profile identifier, along with its details and annotations. If a base ID (i.e., without a version suffix) is 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 follows a "base_id.version" naming scheme.

file_format

Character: Instead of returning an R object, you can directly download the profile matrix as a file in 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 containing the PFM, details, and annotations. If file_format is supplied, the function returns the unparsed file content as a character string.

Corresponding API Resources

"GET https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/"

References

  • Baydar Ovek D, et al. JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models. Nucleic Acids Res. 2026;54(D1):D184-D193; doi: 10.1093/nar/gkaf1209

  • Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx804

  • JASPAR API Documentation

  • Citations note on JASPAR website

See also

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

Examples

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