functional_enrichment-ANY-method {cola} | R Documentation |
Perform functional enrichment on signature genes
## S4 method for signature 'ANY' functional_enrichment(object, id_mapping = guess_id_mapping(object, org_db, verbose), org_db = "org.Hs.eg.db", ontology = "BP", min_set_size = 10, max_set_size = 1000, verbose = TRUE, prefix = "", ...)
object |
A vector of gene IDs. |
id_mapping |
If the gene IDs are not Entrez IDs, a named vector should be provided where the names are the gene IDs and values are the correspoinding Entrez IDs. The value can also be a function that converts gene IDs. |
org_db |
Annotation database. |
ontology |
Following ontologies are allowed: |
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 |
The function enrichment is applied by clusterProfiler, DOSE or ReactomePA packages.
A data frame.
http://bioconductor.org/packages/devel/bioc/vignettes/cola/inst/doc/functional_enrichment.html
# There is no example NULL