functional_enrichment-ConsensusPartition-method: Perform functional enrichment on signature genes
In jokergoo/cola: A Framework for Consensus Partitioning

functional_enrichment-ConsensusPartition-method

R Documentation

Perform functional enrichment on signature genes

Description

Perform functional enrichment on signature genes

Usage

## S4 method for signature 'ConsensusPartition'
functional_enrichment(object, gene_fdr_cutoff = cola_opt$fdr_cutoff, k = suggest_best_k(object, help = FALSE),
    row_km = NULL, id_mapping = guess_id_mapping(rownames(object), org_db, verbose),
    org_db = "org.Hs.eg.db", ontology = "BP",
    min_set_size = 10, max_set_size = 1000,
    verbose = TRUE, prefix = "", ...)

Arguments

`object`	a `ConsensusPartition-class` object from `run_all_consensus_partition_methods`.
`gene_fdr_cutoff`	Cutoff of FDR to define significant signature genes.
`k`	Number of subgroups.
`row_km`	Number of row clusterings by k-means to separate the matrix that only contains signatures.
`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.
`verbose`	Whether to print messages.
`prefix`	Used internally.
`...`	Pass to `functional_enrichment,ANY-method`.