functional_enrichment-ConsensusPartitionList-method: Perform functional enrichment on signature genes

In jokergoo/cola: A Framework for Consensus Partitioning

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
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jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.