geneSim: Semantic Similarity Between two Genes

In YuLab-SMU/GOSemSim: GO-terms Semantic Similarity Measures

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, semData, measure = "Wang", drop = "IEA", combine = "BMA")

Arguments

gene1	Entrez gene id.
gene2	Another entrez gene id.
semData	GOSemSimDATA object
measure	One of "Resnik", "Lin", "Rel", "Jiang" "TCSS" and "Wang" methods.
drop	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
combine	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

Value

list of similarity value and corresponding GO.

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976–978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

See Also

goSim mgoSim mgeneSim clusterSim mclusterSim

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
geneSim("241", "251", semData=d, measure="Wang")

YuLab-SMU/GOSemSim documentation built on April 23, 2024, 11:35 a.m.