functional_enrichment-ANY-method {cola} | 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 which are row names of the original matrix are not Entrez IDs, a named vector should be provided where the names are the gene IDs in the matrix and values are 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`.

### Details

The function enrichment is applied by clusterProfiler, DOSE or ReactomePA packages.

### Value

A data frame.

### Examples

    # There is no example
    NULL

[Package cola version 1.4.1 Index]