goSim {GOSemSim}R Documentation

Semantic Similarity Between Two GO Terms

Description

Given two GO IDs, this function calculates their semantic similarity.

Usage

goSim(GOID1, GOID2, ont = "MF", organism="human", measure="Wang")

Arguments

GOID1 GO ID 1.
GOID2 GO ID 2.
ont One of "MF", "BP", and "CC" subontologies.
organism One of "human", "rat", "mouse", "fly" and "yeast".
measure One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.

Value

goSim Semantic similarity.

References

Wang et al.(2007) A new method to measure the semantic similarity of go terms Bioinformatics (Oxford, England), 23:0 1274–81, May 2007. ISSN 1460-2059 http://www.ncbi.nlm.nih.gov/pubmed/17344234 PMID: 17344234

P W Lord et al.(2003) Semantic similarity measures as tools for exploring the gene ontology Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, 2003:601-12, ISSN 1793-5091 http://www.ncbi.nlm.nih.gov/pubmed/12603061 PMID: 12603061

See Also

mgoSim geneSim mgeneSim clusterSim mclusterSim

Examples

        goSim("GO:0043121", "GO:0019838", measure="Wang")
        goSim("GO:0043121", "GO:0019838", ont="MF", organism="human", measure="Wang")

[Package GOSemSim version 1.2.0 Index]