GOSim (version 1.10.0)

setOntology: Set an ontology as base for subsequent computations.

Description

Sets the ontology that all subsequent computations are based on and loads the information content of all GO terms within this ontology. At load time of the library the default ontology is "BP". Furtherm, on running this function the environment GOSimEnv is reinitialized, i.e. all global settings or parameters used in the library are reset to their default values.

Usage

setOntology(ont = "BP", loadIC=TRUE, DIR=NULL)

Arguments

ont

the ontology to use ("BP","MF","CC")

loadIC

Should the corresponding file with precomputed IC-values be loaded? Default: TRUE. WARNING: If the file is not loaded, no calculations can be performed! This might only be useful, if you want to recalculate IC values.

DIR

If not null, load file from this directory. Otherwise the version installed in GOSim's data directory is used.

Value

none.

Details

The following ontologies can be used:

"BP"

biological process

"MF"

molecular function

"CC"

cellular component

Examples

 # set ontology to "molecular function"

 setOntology("MF")
 # calculate Resnik similarity of two GO terms within this ontology
 getTermSim(c("GO:0004060","GO:0003867"),method="Resnik")