GO_enrichment-ConsensusPartitionList-method {cola}R Documentation

Perform Gene Ontology Enrichment on Signature Genes

Description

Perform Gene Ontology Enrichment on Signature Genes

Usage

## S4 method for signature 'ConsensusPartitionList'
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", ontology = c("BP", "MF", "CC"),
    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

"BP": biological processes, "MF": molecular functions, "CC": cellular components.

min_set_size

The minimal size of the GO gene sets.

max_set_size

The maximal size of the GO gene sets.

Details

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

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

Value

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

Examples

# There is no example
NULL


[Package cola version 1.0.1 Index]