mgoSim {GOSemSim}R Documentation

Semantic Similarity Between two GO terms lists

Description

Given two GO term sets, this function will calculate the semantic similarity between them, and return their semantic similarity

Usage

mgoSim(GO1, GO2, ont="MF", organism="human", measure="Wang")

Arguments

GO1 A set of go terms.
GO2 Another set of go terms.
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

mgoSim 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

goSim geneSim mgeneSim clusterSim mclusterSim

Examples

        go1 <- c("GO:0004022", "GO:0004024", "GO:0004023")
        go2 <- c("GO:0009055", "GO:0020037")
        mgoSim("GO:0003824", go2, measure="Wang")
        mgoSim(go1, go2, ont="MF", organism="human", measure="Wang")

[Package GOSemSim version 1.2.0 Index]