setOntology: Set an ontology as base for subsequent computations.

In GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis

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.

Details

The following ontologies can be used:

"BP"

biological process

"MF"

molecular function

"CC"

cellular component

Value

none.

Author(s)

Holger Froehlich

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")

GOSim documentation built on Nov. 8, 2020, 11:05 p.m.