functional_enrichment-ConsensusPartitionList-method {cola} | R Documentation

## Perform functional enrichment on signature genes

### Description

Perform functional enrichment on signature genes

### Usage

    ## S4 method for signature 'ConsensusPartitionList'
    functional_enrichment(object, gene_fdr_cutoff = cola_opt$fdr_cutoff,
        id_mapping = guess_id_mapping(rownames(object), org_db, FALSE),
        org_db = "org.Hs.eg.db", ontology = "BP",
        min_set_size = 10, max_set_size = 1000, ...)

### Arguments

`object` | A `ConsensusPartitionList-class` object from `run_all_consensus_partition_methods`.
`gene_fdr_cutoff` | Cutoff of FDR to define significant signature genes.
`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` | See corresponding argumnet in `functional_enrichment,ANY-method`.
`min_set_size` | The minimal size of the gene sets.
`max_set_size` | The maximal size of the gene sets.
`...` | Pass to `functional_enrichment,ANY-method`.

### Details

For each method, the signature genes are extracted based on the best k.

It calls `functional_enrichment,ConsensusPartition-method` on the consensus partitioning results for each method.

For how to control the parameters of functional enrichment, see help page of `functional_enrichment,ANY-method`.

### Value

A list where each element in the list corresponds to enrichment results from a single method.

### See Also

http://bioconductor.org/packages/devel/bioc/vignettes/cola/inst/doc/functional_enrichment.html

### Examples

    # There is no example
    NULL

[Package cola version 1.8.1 Index]