calcICs {GOSim}R Documentation

Calculate information contents of GO terms.

Description

Recalculates the information content of all GO terms.

Usage

calcICs()

Arguments

none

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.

Value

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.

See Also

setEvidenceLevel

Examples

              
## 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 ...

[Package GOSim version 1.1.5.4 Index]