TCSSGeneSim: Topological Clustering Semantic Similarity(TCSS) Between two Genes
Description
Given two genes, this function will calculate the TCSS between them
Usage
TCSSGeneSim(gene1, gene2, ont = "MF", organism = "yeast", drop = "IEA")
Arguments
gene1
Entrez gene id.
gene2
Another entrez gene id.
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. Jain and G. Bader, "An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology", BMC Bioinformatics, vol. 11, no. 1, p. 562, 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.