functional_enrichment-HierarchicalPartition-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 '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

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