Get PANTHER database Information

Using this function you can retrieve a list of available organisms, annotation datasets, families, and pathways which are supported in PANTHER.

Usage

rba_panther_info(what, organism_chr_loc = FALSE, families_page = 1, ...)

Arguments

what

what information to retrieve? should be one of:

• "organisms": Retrieve supported organisms in PANTHER.

• "datasets": Retrieve available annotation datasets.

• "families": Retrieve available family IDs.

• "species_tree": Retrieve PANTHER's species tree.

• "pathways" Retrieve available pathway IDs.

organism_chr_loc

(Logical) (only when 'what = "organisms"') If TRUE, only organisms with chromosome location will be returned. If FALSE (default), all organisms will be returned.

families_page

(Numeric) (only when 'what = "families"') Family information is very long, so results are returned in pages of up to 1,000 families. Use a positive whole number to define the page to retrieve.

...

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

Value

For families, a list containing family information, the requested page, and the total number of pages. For the species tree, a list; otherwise a data frame with pertinent information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/supportedgenomes"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedannotdatasets"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedpantherfamilies"
"GET https://www.pantherdb.org/services/oai/pantherdb/supportedpantherpathways"
"GET https://www.pantherdb.org/services/oai/pantherdb/speciestree"

References

• Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H. (2022) PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science, 31(1), 8–22. https://doi.org/10.1002/pro.4218

• PANTHER Services Details

• Citations note on PANTHER website

See also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_genome(), rba_panther_homolog(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

# \donttest{
rba_panther_info(what = "organisms")
# }
# \donttest{
rba_panther_info(what = "families", families_page = 4)
# }