GOSim (version 1.10.0)

calcICs: Calculate information contents of GO terms.

Description

Recalculates the information content of all GO terms.

Usage

calcICs(DIR=".")

Arguments

DIR

directory where to put the resulting files

Value

Puts a file named "ICs.rda" in directoy DIR. It can be used afterwards by calling setOntology.

Details

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.

See Also

setEvidenceLevel

Examples

  	
	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 ...