GO_enrichment-ConsensusPartitionList-method {cola} | R Documentation |
Perform Gene Ontology Enrichment on Signature Genes
## S4 method for signature 'ConsensusPartitionList' GO_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 = c("BP", "MF", "CC"), min_set_size = 10, max_set_size = 1000)
object |
A |
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 |
"BP": biological processes, "MF": molecular functions, "CC": cellular components. |
min_set_size |
The minimal size of the GO gene sets. |
max_set_size |
The maximal size of the GO gene sets. |
For each method, the signature genes are extracted based on the best k.
It calls GO_enrichment,ConsensusPartition-method
on the consensus partitioning results for each method.
A list where each element in the list corresponds to enrichment results from a single method.
# There is no example NULL