GO_enrichment-HierarchicalPartition-method {cola} | R Documentation

## Perform Gene Ontology Enrichment on Signature Genes

### Description

Perform Gene Ontology Enrichment on Signature Genes

### Usage

    ## S4 method for signature 'HierarchicalPartition'
    GO_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",
        min_set_size = 10, max_set_size = 1000)

### Arguments

`object` | A `HierarchicalPartition-class` object.
`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.
`min_set_size` | The minimal size of the GO gene sets.
`max_set_size` | The maximal size of the GO gene sets.

### Details

On each node of the partition hierarchy, the signature genes are extracted based on the best k.

It calls `GO_enrichment,ConsensusPartition-method` on the consensus partitioning results on each node.

### Value

A list where each element in the list corresponds to enrichment results on a node.

### Examples

    # There is no example
    NULL

[Package cola version 1.0.1 Index]