pickWGCNAParam: Pick WGCNA parameters

In stringgaussnet: PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

Description

A function to help in choosing the WGCNA soft threshold parameter parameter, with a series of plot.

Usage

pickWGCNAParam(DEGeneExpr, Alphas = c(c(1:10), seq(from = 12, to = 20, by = 2)),
	AThreshold = 0.85, interactiveMode = T)

Arguments

DEGeneExpr	Object of class DEGeneExpr
Alphas	The series of soft threshold parameters to test
AThreshold	Adjacency threshold to be displayed on plots
interactiveMode	Boolean variable indicating whether the plots are in interactive mode. If false, it is useful for automatically saving plots in a single pdf file.

Details

Firstly, this function plots adjacency scores as a function of similarity scores, with different soft threshold parameters. Secondly, it displays network connectivity with different alpha values (with horizontal dashed lines at 0.05, 0.1 and 0.25 of total number of possible edges). In the same way, the next plots display maximal p-values, mean node connectivities, minimal spearman's rhos as a function of alpha values. Next plots show distributions of spearman's rhos (absolute values) and of p-values (logarithm scale). Finally, we can see a plot displaying spearman's p-values as a function of absolute values of rhos, with an horizontal dash line representing a p-value of 0.05 and a vertical one showing the rho for which we are the nearest to a p-value of 0.05.

See Also

WGCNANet, WGCNANet.default, getWGCNANet, print.WGCNANet, summary.WGCNANet, export.WGCNANet, compareGaussNetworks

Examples

# data(SpADataExpression)
# data(SpADEGenes)
# SpAData<-DEGeneExpr(t(SpADataExpression),SpADEGenes)

# NodesForSIMoNe<-rownames(SpADEGenes)[1:17]
# GaussianSpAData<-DEGeneExpr(t(SpADataExpression[NodesForSIMoNe,]),SpADEGenes[NodesForSIMoNe,])

# pickWGCNAParam(GaussianSpAData)
# GlobalWGCNANet<-getWGCNANet(GaussianSpAData)
# print(GlobalWGCNANet,5)
# summary(GlobalWGCNANet)
# plot(GlobalWGCNANet)
# export(GlobalWGCNANet,"GlobalWGCNANet",T)

# compareGaussNetworks(GlobalSIMoNeNet,GlobalWGCNANet,c("SIMoNe","WGCNA"))

stringgaussnet documentation built on May 29, 2017, 10:50 a.m.