setOntology {GOSim}R Documentation

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")

Arguments

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

Details

The following ontologies can be used: begin{ldescription}

"BP"
biological process
"MF"
molecular function
"CC"
cellular component
end{ldescription}

Value

none.

Author(s)

Holger Froehlich

Examples

 # set ontology to "molecular function"
## Not run: 
 setOntology("MF")
 # calculate Resnik similarity of two GO terms within this ontology
 getTermSim(c("GO:0004060","GO:0003867"),method="Resnik")
## End(Not run)

[Package GOSim version 1.0.2 Index]