Description Usage Arguments Details Value Note Author(s) References See Also Examples
Determine the threshold parameter which will result in a network with optimal scale-free fitness.
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simMat |
The GO-similairty matrix. Missing and negative entries are not allowed. The gene names should be assigned to the row and column names. |
rhovec |
a vector of candidate thresholds, or if NULL, a set of thresholds chosen according to the range of the similarity matrix. |
The scale-free fitness measure is based on linear-regression-based R-squared goodness-of-fit measure.
A list, with elements:
criterion |
a summary table of the candidate thresholds' resulting fits. |
bestrho |
The candidate threshold with the highest R-squared. |
Note that certain GO-similarity measures are unbounded (e.g. the Resnik similarity). This code will not normalize the similarity matrix, and rhovec, if supplied, should be chosen according to the range of the GO-similarity values inside simMat.
Billy Chang
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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