setOntology {GOSim} | R Documentation |
Sets the ontology that all subsequent computations are based on and loads the information content of all GO terms within this ontology. At load time of the library the default ontology is "BP". Furtherm, on running this function the environment GOSimEnv is reinitialized, i.e. all global settings or parameters used in the library are reset to their default values.
setOntology(ont = "BP", loadIC=TRUE)
ont |
the ontology to use ("BP","MF","CC") |
loadIC |
Should the corresponding file with precomputed IC-values be loaded? Default: TRUE. WARNING: If the file is not loaded, no calculations can be performed! This might only be useful, if you want to recalculate IC values. |
The following ontologies can be used:
none.
Holger Froehlich
# set ontology to "molecular function" ## Not run: setOntology("MF") # calculate Resnik similarity of two GO terms within this ontology getTermSim(c("GO:0004060","GO:0003867"),method="Resnik") ## End(Not run)