functional_enrichment-ConsensusPartition-method {cola} | R Documentation |
Perform functional enrichment on signature genes
## 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, ...)
object |
a |
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 |
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 |
For how to control the parameters of functional enrichment, see help page of functional_enrichment,ANY-method
.
A list of data frames which correspond to results for the functional ontologies:
http://bioconductor.org/packages/devel/bioc/vignettes/cola/inst/doc/functional_enrichment.html
# There is no example NULL