rba_panther_info: Get PANTHER database Information

In rbioapi: User-Friendly R Interface to Biologic Web Services' API

Get PANTHER database Information

Description

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 the 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) every organisms will be returned.
families_page	(Numeric) (only when 'what = "families"') Family information is very long, so results are paginated. Use this argument to define the page to retrieve.
...	rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

For families and species tree, a list and 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

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See Also

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

Examples

rba_panther_info(what = "organisms")


rba_panther_info(what = "families", families_page = 4)

rbioapi documentation built on April 4, 2025, 5:04 a.m.