You can use this function to list the JASPAR matrix profiles that match your search query, or run the function without any arguments to return a list of every matrix profile available in the latest release.
Usage
rba_jaspar_matrix_search(
term = NULL,
tf_name = NULL,
tf_class = NULL,
tf_family = NULL,
tax_group = NULL,
tax_id = NULL,
data_type = NULL,
collection = NULL,
release = 2022,
only_last_version = FALSE,
order = NULL,
page_size = 1000,
page = 1,
...
)
Arguments
- term
Character: A search term.
- tf_name
Character: Transcription factor names (Case-sensitive).
- tf_class
Character: Transcription factor class
- tf_family
Character: Transcription factor family
- tax_group
Character: Taxonomic group. Use
rba_jaspar_taxons
to get a list of supported Taxonomic groups.- tax_id
Numeric: NCBI taxonomic Identifier of species. Use
rba_jaspar_species
to get a list of supported Species.- data_type
Character: Type of the data (i.e The Methodology used for matrix construction). For example: "ChIP-seq", "PBM"
- collection
Character: JASPAR matrix profile collection name. USE
rba_jaspar_collections
to get a list of collection names.- 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.
- 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.
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.
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.
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
See also
Other "JASPAR":
rba_jaspar_collections_matrices()
,
rba_jaspar_collections()
,
rba_jaspar_matrix_versions()
,
rba_jaspar_matrix()
,
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_search(term = "FOX")
rba_jaspar_matrix_search(tf_name = "FOXP3")
rba_jaspar_matrix_search(tf_name = "FOXP3", only_last_version = TRUE)
rba_jaspar_matrix_search(tf_class = "Zipper-Type")
rba_jaspar_matrix_search(tax_group = "insects")
rba_jaspar_matrix_search(page_size = 100)
# }