Perform functional enrichment on signature genes

Perform functional enrichment on signature genes

# S4 method for 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.

Examples

# There is no example
NULL
#> NULL