Description Usage Arguments Value References Examples
View source: R/fit.structure.R
The function is to used to calcuate the scale-free or modularity fitness of networks. The scale-free fitness is calcuated as
-R^2\times slope of the fit index of the model. Please refer to the package WGCNA
[1,2] for details.The fitness of modularity is computed
using igraph
package [3].
1 | fit.structure(edgelist, method = "scale-free")
|
edgelist |
a data frame of network edge list, with regulators in first column, target genes in second column and edge weights in third column. |
method |
a character string used to calculate the structural fitness. Options are "scale-free" and "modularity". |
fit.structure
returns a numeric value measures the structural fitness.
[1] Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559.
[2] Zhao W, Langfelder P, Fuller T, Dong J, Li A, Hovarth S: Weighted gene coexpression network analysis: state of the art. J Biopharm Stat 2010, 20(2):281-300.
[3] Csardi G, Nepusz T: The igraph software package for complex network research. InterJournal 2006, Complex Systems:1695.
1 2 3 4 5 6 | library(RLowPC)
data(gnwdata)
edgelist<-gnwdata$size500$net1
edgelist[,3]<-1
fit.structure(edgelist,method='scale-free')
fit.structure(edgelist,method='modularity')
|
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