Perform functional enrichment on signature genes

# S4 method for HierarchicalPartition
functional_enrichment(object, merge_node = merge_node_param(),
    gene_fdr_cutoff = cola_opt$fdr_cutoff,
    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, ...)

Arguments

object: a HierarchicalPartition-class object from hierarchical_partition.
merge_node: Parameters to merge sub-dendrograms, see merge_node_param.
gene_fdr_cutoff: Cutoff of FDR to define significant signature genes.
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.
...: Pass to functional_enrichment,ANY-method.

Details

For how to control the parameters of functional enrichment, see help page of functional_enrichment,ANY-method.

Value

A list of data frames which correspond to results for the functional ontologies:

Examples

# There is no example
NULL
#> NULL