Using this function, you can retrieve Orthologs, MSA or Tree topology information of a given PANTHER family.

rba_panther_family(id, what, target_organisms = NULL, ...)

Arguments

id

Panther family id.

what

What to retrieve? One of:

  • "ortholog": Orthologs ('LDO' for least diverged and 'O' for more diverged).

  • "msa": Multiple Sequence Alignment Information,

  • "tree": Tree topology and nodes attributes.

target_organisms

(numeric) NCBI taxon ID(s) to filter the results. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.

...

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

Value

For trees a list and otherwise a data frame with the requested family's information.

Corresponding API Resources

"GET http://www.pantherdb.org/services/oai/pantherdb/familyortholog"
"GET http://www.pantherdb.org/services/oai/pantherdb/familymsa"
"GET http://www.pantherdb.org/services/oai/pantherdb/treeinfo"

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_family("PTHR10000", what = "ortholog")
# }