calcICs {GOSim} | R Documentation |
Recalculates the information content of all GO terms.
calcICs(DIR=".")
DIR |
directory where to put the resulting files |
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
directoy DIR. It can be used afterwards by calling setOntology
.
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() # --> this may take some time ...