WGCNA - Network construction and module detection
0
0
Entering edit mode
Recep • 0
@7c8fd686
Last seen 10 weeks ago
Germany

Hello im using WGCNA to cluster genes. I got this tutorial code from here.

I got the concept and how to choice the power but I am wondering, how can i select the parameters of power (like here from 10 to 30 and c is between 1 and 10) and h, which is here 0.90.

    powers = c(c(1:10), seq(from =10, to=30, by=1)) #choosing a set of soft-thresholding powers
    sft = pickSoftThreshold(datExpr, powerVector=powers, verbose =5, networkType="signed") #call network enter code heretopology analysis function

    sizeGrWindow(9,5)
    par(mfrow= c(1,2))
    cex1=0.9
    plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab= "Soft Threshold (power)", ylab="Scale Free Topology Model Fit, signed R^2", type= "n", main= paste("Scale independence"))
    text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers, cex=cex1, col="red")
    abline(h=0.90, col="red")
    plot(sft$fitIndices[,1], sft$fitIndices[,5], xlab= "Soft Threshold (power)", ylab="Mean Connectivity", type="n", main = paste("Mean connectivity"))
    text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1, col="red")

    #from this plot, we would choose a power of 18 becuase it's the lowest power for which the scale free topology index reaches 0.90
gene Clustering wgcna flashclust • 183 views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 346 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6