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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.

Usage

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. Note that you should enter the "id" of the dataset, not its label (e.g. entering "biological_process" is incorrect, you should rather enter "GO:0008150").

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 parameters and results. If the analysis was successful, the results data frame are returned in the "results" element within the list. Otherwise, an error message will be returned under the "search$error" element in the returned list.

Corresponding API Resources

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

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

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)
# }