GO_enrichment-ANY-method {cola} | R Documentation |
Perform Gene Ontology Enrichment on Signature Genes
## S4 method for signature 'ANY' GO_enrichment(object, id_mapping = guess_id_mapping(object, org_db, verbose), org_db = "org.Hs.eg.db", ontology = c("BP", "MF", "CC"), min_set_size = 10, max_set_size = 1000, verbose = TRUE, ...)
object |
A vector of gene IDs. |
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. |
verbose |
Whether to print messages. |
... |
Other arguments. |
A list of three data frames which correspond to results for three GO catalogues:
BP
: biological processes
MF
: molecular functions
CC
: cellular components
# There is no example NULL