IntelliGOGeneSim: IntelliGO Semantic Similarity Between two Genes

In ppiPre: Predict Protein-Protein Interactions Based on Functional and Topological Similarities

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

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

Author(s)

Yue Deng <[e-mail]>

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.

See Also

TCSSGeneSim

Examples

  #IntelliGOGeneSim("1134", "1145", ont="MF", organism="human")
  #IntelliGOGeneSim("YOL001W", "YPL031C", ont="MF", organism="yeast")

ppiPre documentation built on May 30, 2017, 4:33 a.m.