functional_enrichment-ANY-method: Perform functional enrichment on signature genes
In jokergoo/cola: A Framework for Consensus Partitioning

functional_enrichment-ANY-method

R Documentation

Perform functional enrichment on signature genes

Description

Perform functional enrichment on signature genes

Usage

## S4 method for signature 'ANY'
functional_enrichment(object,
    id_mapping = guess_id_mapping(object, org_db, verbose),
    org_db = "org.Hs.eg.db", ontology = "BP",
    min_set_size = 10, max_set_size = 1000,
    verbose = TRUE, prefix = "", ...)

Arguments

`object`	A vector of gene IDs.
`id_mapping`	If the gene IDs are not Entrez IDs, a named vector should be provided where the names are the gene IDs and values are the correspoinding Entrez IDs. The value can also be a function that converts gene IDs.
`org_db`	Annotation database.
`ontology`	Following ontologies are allowed: `BP`, `CC`, `MF`, `KEGG`, `Reactome`. `MSigDb` with the gmt file set by `gmt_file` argument, or `gmt` for general gmt gene sets.
`min_set_size`	The minimal size of the gene sets.
`max_set_size`	The maximal size of the gene sets.
`verbose`	Whether to print messages.
`prefix`	Used internally.
`...`	Pass to `enrichGO`, `enrichKEGG`, `enricher`, `enrichDO` or `enrichPathway`.