Using this function you can use PANTHER services to perform over-representation enrichment analysis. This statistical test will compare your input genes to a set of defined gene lists to determine if they are over/under-represented.

rba_panther_enrich(
  genes,
  organism,
  annot_dataset,
  test_type = "FISHER",
  correction = "FDR",
  cutoff = NULL,
  ref_genes = NULL,
  ref_organism = NULL,
  ...
)

Arguments

genes

Character vector of genes identifiers with maximum length of 10000. Can be any of: Ensemble gene ID, Ensemble protein ID, Ensemble transcript ID, Entrez gene ID, gene symbol, NCBI GI, HGNC ID, International protein index ID, NCBI UniGene ID, UniProt accession and/or UniProt ID.

organism

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

annot_dataset

A PANTHER dataset ID to test your input against it. run rba_panther_infowith argument 'what = "datasets"' to get a list of PANTHER's supported datasets.

test_type

statistical test type to calculate the p values. either "FISHER" (default) or "BINOMIAL".

correction

p value correction method. either "FDR" (default), "BONFERRONI" or "NONE".

cutoff

(Numeric) (Optional) a threshold to filter the results. if correction is "FDR", the threshold will be applied to fdr column's values; if otherwise, the threshold will be applied to p value column.

ref_genes

(Optional) A set of genes that will be used as the test's background (reference/universe) gene set. If no value supplied, all of the genes in specified organism will be used. maximum length and supported IDs are the same as 'genes' argument.

ref_organism

(Optional) if 'ref_genes' is used, you can specify the organisms which correspond to your supplied IDs in 'ref_genes' argument. see 'organism' argument for supported values.

...

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

Value

A list with the prov

Corresponding API Resources

"POST http://www.pantherdb.org/services/oai/pantherdb/enrich/overrep"

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_enrich(genes = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42",
        "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
    organism = 9606, annot_dataset = "GO:0008150",
    cutoff = 0.01)
# }