getTermSim {GOSim} | R Documentation |
Returns the pairwise similarities between GO terms. Different calculation method are implemented.
getTermSim(termlist, method = "JiangConrath", verbose = TRUE)
termlist |
character vector of GO terms |
method |
one of ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin") |
verbose |
print out various information or not |
Currently the following methods for computing GO term similarities are implemented: begin{ldescription}
setEnrichmentFactors
term1
and term2
(ICshare) [5]n x n matrix (n = number of GO terms) with similarities between GO terms scaled to [0,1]
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")
Holger Froehlich
[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
getMinimumSubsumer
,
getDisjCommAnc
, setEnrichmentFactors
,
setOntology
# 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")