GOKEGGSims: GO- and KEGG- based Similarities Between two Genes

Description Usage Arguments Author(s) References See Also Examples

View source: R/GOKEGGSims.r

Description

Given two genes, this function will calculate KEGG-based similarity and three GO-based similarities between them

Usage

1
GOKEGGSims(gene1, gene2, organism = "yeast", drop = "IEA")

Arguments

gene1

Entrez gene id.

gene2

Another entrez gene id.

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.

Author(s)

Yue Deng <anfdeng@163.com>

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] J. Z. Wang, Z. Du, R. Payattakool, P. S. Yu, and C.-F. Chen, "A new method to measure the semantic similarity of GO terms", Bioinformatics, vol. 23, no. 10, pp. 1274-1281, May. 2007.

[3] 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.

[4] 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.

See Also

TCSSGeneSim IntelliGOGeneSim GOKEGGSimsFromFile

Examples

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2
  #GOKEGGSims("1134", "1145", organism = "human", drop = "IEA")
  #GOKEGGSims("YER133W", "YBR045C", organism = "yeast")

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