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Get PANTHER database Information

Source: R/panther.R
rba_panther_info.Rd

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

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