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Get PANTHER Families and Sub-Families

Source: R/panther.R
rba_panther_family.Rd

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

Usage

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

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_homolog(), rba_panther_info(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

# \donttest{
rba_panther_family("PTHR10000", what = "ortholog")
# }