calcICs {GOSim} | R Documentation |
Recalculates the information content of all GO terms.
calcICs()
none
This functions should only be invoked, if one wants to calculate the information content for GO terms with respect to combinations of evidence codes other than the precomputed ones or, if a new version of the organism annotation packages has been installed. By default the information contents are precomputed using all evidence codes and evidence codes "IMP, IGI, IDA, IEP, IPI" together.
Puts a file named "ICs<ontology><organism><evidence levels>.rda" in the current
directoy. This file has then to be moved into the data directory of
GOSim. It can be used afterwards by calling setOntology
.
Sometimes it is necessary to switch to the GOSim directory for this purpose.
## Not run: setEvidenceLevel("IMP") setOntology("CC", loadIC=FALSE) # important: setOntology assumes that the IC file already exists. To prevent an error message we need the second argument calcICs() ## End(Not run) # --> this may take some time ...