IntelliGOGeneSim: IntelliGO Semantic Similarity Between two Genes
Description
Given two genes, this function will calculate the IntelliGO Semantic Similarity between them
Usage
IntelliGOGeneSim(gene1, gene2, w1 = 1, w2 = 1, ont = "MF",
organism = "yeast", drop = "IEA")
Arguments
gene1
Entrez gene id.
gene2
Another entrez gene id.
w1
EC weight
w2
EC weight
ont
One of "MF", "BP", and "CC" subontologies.
organism
One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "ecolik12", "ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat", "rhesus", "worm", "xenopus", "yeast" and "zebrafish."
drop
A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
Value
geneSimSemantic similarity.
GO1Corresponding GO terms for gene1.
GO2Corresponding GO terms for gene2.
References
[1] S. Benabderrahmane, M. Smail-Tabbone, O. Poch, A. Napoli, and M.-D. Devignes, "IntelliGO: a new vector-based semantic similarity measure including annotation origin", BMC Bioinformatics, vol. 11, no. 1, p. 588, 2010.
[2] G. Yu, F. Li, Y. Qin, X. Bo, Y. Wu, and S. Wang, "GOSemSim: an R package for measuring semantic similarity among GO terms and gene products", Bioinformatics, vol. 26, no. 7, pp. 976-978, Apr. 2010.