getTermSim {GOSim}R Documentation

Get pairwise GO term similarities.

Description

Returns the pairwise similarities between GO terms. Different calculation method are implemented.

Usage

getTermSim(termlist, method = "JiangConrath", verbose = TRUE)

Arguments

termlist character vector of GO terms
method one of ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
verbose print out various information or not

Details

Currently the following methods for computing GO term similarities are implemented: begin{ldescription}

"Resnik"
information content of minimum subsumer (ICms) [1]
"JiangConrath"
1 - min(1, IC(term1) - 2ICms + IC(term2)) [2]
"Lin"
frac{2ICms}{(IC(term1) + IC(term2))} [3]
"CoutoEnriched"
FuSSiMeg enriched term similarity by Couto et al. [4]. Requires enrichement factors to be set by setEnrichmentFactors
.
"CoutoResnik"
average information content of common disjunctive ancestors of term1 and term2 (ICshare) [5]
"CoutoJiangConrath"
1 - min(1, IC(term1) -2ICshare + IC(term2)) [5]
"CoutoLin"
frac{2ICshare}{(IC(term1) + IC(term2))} [5]
end{ldescription}

Value

n x n matrix (n = number of GO terms) with similarities between GO terms scaled to [0,1]

Note

All calculations use normalized information contents for each GO term. Normalization is achieved by dividing each information content by the maximum information content within the currently set ontology ("BP","MF","CC")

Author(s)

Holger Froehlich

References

[1] P. Resnik, Using Information Content to evaluate semantic similarity in a taxonomy, Proc. 14th Int. Conf. Artificial Intel., 1995 newline [2] J. Jiang, D. Conrath, Semantic Similarity based on Corpus Statistics and Lexical Taxonomy, Proc. Int. Conf. Research in Comp. Ling., 1998 newline [3] D. Lin, An Information-Theoretic Definition of Similarity, Proc. 15th Int. Conf. Machine Learning, 1998 newline [4] F. Couto, M. Silva, P. Coutinho, Implementation of a Functional Semantic Similarity Measure between Gene-Products, DI/FCUL TR 03-29, Department of Informatics, University of Lisbon, 2003 newline [5] Couto, F.; Silva, M. & Coutinho, P., Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors, Conference in Information and Knowledge Management, 2005

See Also

getMinimumSubsumer, getDisjCommAnc, setEnrichmentFactors, setOntology

Examples

 # setOntology("BP")

 # Lin's method
 getTermSim(c("GO:0006955","GO:0007584"),method="Lin")
 # Couto's method combined with Jiang-Conrath distance
 getTermSim(c("GO:0006955","GO:0007584"),method="CoutoJiangConrath") 

 # set enrichment factors
 setEnrichmentFactors(alpha=0.1,beta=0.5) 
 getTermSim(c("GO:0006955","GO:0007584"),method="CoutoEnriched")

[Package GOSim version 1.0.2 Index]