getGNET: Gene Network Construction by Similarity-Thresholding
In GOGANPA: GO-Functional-Network-based Gene-Set-Analysis

Description Usage Arguments Value Note Author(s) References See Also Examples

Construct a gene network by linking gene-pairs with GO similarity above a chosen threshold.

1	getGNET(simMat, rho)

`simMat`	The GO-similairty matrix. Missing and negative entries are not allowed. The gene names should be assigned to the row and column names.
`rho`	The threshold, chosen e.g. by `selectRho`. Gene-pairs with similarity above the threshold will be linked.

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.

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.

selectRho

#Not to Run
data("simMatSmall",package="GOGANPA")
gNET <- getGNET(simMatSmall,rho=0.7)
hist(sapply(gNET,length)) # network connectivities (excluding unconnected genes)