Gene Network Construction by Similarity-Thresholding

Share:

Description

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

Usage

1
getGNET(simMat, rho)

Arguments

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.

Value

A list, where each element contains the names of the genes connected to the corresponding gene indicated by the element-header.

Note

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.

Author(s)

Billy Chang

References

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.

See Also

selectRho

Examples

1
2
3
4
#Not to Run
data("simMatSmall",package="GOGANPA")
gNET <- getGNET(simMatSmall,rho=0.7)
hist(sapply(gNET,length)) # network connectivities (excluding unconnected genes)