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]