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

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.

  • "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, a list and otherwise a data frame with pertinent information.

Corresponding API Resources

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

References

  • Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2019). PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic acids research, 47(D1), D419-D426.

  • Mi, H., Muruganujan, A., Huang, X., Ebert, D., Mills, C., Guo, X., & Thomas, P. D. (2019). Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v. 14.0). Nature protocols, 14(3), 703-721.

  • PANTHER Services Details

See also

Examples

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