Construct a gene network by linking gene-pairs with GO similarity above a chosen threshold.
The GO-similairty matrix. Missing and negative entries are not allowed. The gene names should be assigned to the row and column names.
The threshold, chosen e.g. by
A list, where each element contains the names of the genes connected to the corresponding gene indicated by the element-header.
Note that certain GO-similarity measures are unbounded (e.g. the Resnik similarity). This code will not normalize the similarity matrix, and rho should therefore be chosen according to the range of the GO-similarity values inside simMat.
Chang, B., Kustra, R. and Tian, WD (2012) Functional-Network-based Gene Set Analysis using Gene Ontology. Submitted.
Zhang, B. and Horvath, S. (2005) A General Framework for Weighted Gene Co-Expression Network Analysis. Statistical Applications in Genetics and Molecular Biology. 4:1:A17.
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