Retrieve Genes from a PANTHER Genome — rba_panther_genome • rbioapi

Retrieve one page of genes and their associated information for a genome supported by PANTHER. Each page contains up to 1,000 genes.

Usage

rba_panther_genome(organism, page, ...)

Arguments

organism: (numeric) NCBI taxon ID. Run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.
page: (numeric) The results page to retrieve. Pages contain up to 1,000 genes and are numbered starting from 1.
...: rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list with the following elements:

gene: A data frame with one row per returned gene. Fields are kept as returned by PANTHER, with annotation information in nested columns.
page: The retrieved page.
pages_count: The total number of available pages.
number_of_genes_in_genome: The total number of genes in the genome.
product: PANTHER product source and version information.
search_type: The search type reported by PANTHER.

Corresponding API Resources

"POST https://www.pantherdb.org/services/oai/pantherdb/downloadgenome"

References

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H. (2022) PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science, 31(1), 8–22. https://doi.org/10.1002/pro.4218
PANTHER Services Details
Citations note on PANTHER website

See also

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

Examples

# \donttest{
rba_panther_genome(organism = 9606, page = 1)
# }