geneSim {GOSemSim}R Documentation

Semantic Similarity Between two Genes

Description

Given two genes, this function will calculate the semantic similarity between them, and return their semantic similarity and the corresponding GO terms

Usage

        geneSim(gene1, gene2, ont = "MF", organism="human",measure="Wang",  drop= "IEA")

Arguments

gene1 Entrez gene id.
gene2 Another entrez gene id.
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.
drop A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.

Value

geneSim Semantic similarity.
GO1 Corresponding GO terms for gene1.
GO2 Corresponding GO terms for gene2.

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 mgoSim mgeneSim clusterSim mclusterSim

Examples

        geneSim("241", "2561", ont="MF", organism="human", measure="Wang")
        geneSim("snR18", "YPR062W", ont="MF", organism="yeast", measure="Wang")

[Package GOSemSim version 1.2.0 Index]