calcICs {GOSim} | R Documentation

## 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

### 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 directoy DIR. It can be used afterwards by calling `setOntology`.

### 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 ...

[Package GOSim version 1.32.0 Index]