Gene Network Construction by Similarity-Thresholding

Description

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

Usage

getGNET(simMat, rho)

Arguments

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

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GOGANPA)
Loading required package: GANPA
Loading required package: GANPAdata
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust


==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GOGANPA/getGNET.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGNET
> ### Title: Gene Network Construction by Similarity-Thresholding
> ### Aliases: getGNET
> 
> ### ** Examples
> 
> #Not to Run
> data("simMatSmall",package="GOGANPA")
> gNET <- getGNET(simMatSmall,rho=0.7)
GOGANPA ignore self-links, diagonal entries of simMat set to 0. 
> hist(sapply(gNET,length)) # network connectivities (excluding unconnected genes)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>