calculate Gene Significance

[bsb2014]

Hi, Narges 1) is there any way to extract the data used for the module-trait plotting?

2) How to extract genes with their MM and GS scores in each module?

Thanks!

[nargesr]

Hi @bsb2014

1. you can extract the correlation using self. moduleTraitCor and corresponding p-value from self. moduleTraitPvalue.

2. can you explain more about what you mean by MM and GS scores?

best, Narges

[bsb2014]

Thanks for your prompt response.

GS : Gene Significance MM: Module Membership

[bsb2014]

Hi Narges

I am a newbie in Python, could you please give me more help with the self.moduleTraitCor/self.moduleTraitPvalue?

I tried the codes below

pyWGCNA_ASM1 = PyWGCNA.readWGCNA("ASM.p") pyWGCNA_ASM1.self. moduleTraitCor.head(5)

and got an error saying [AttributeError: 'WGCNA' object has no attribute 'self']

Thanks

[nargesr]

for module membership, you can use this function called: CalculateSignedKME()

Unfortunately, I didn’t implement the GS yet, if you know how to calculate it and you can send it to me as a function I would be happy to add it to the PyWGCNA.

self would be the name of your object which in your case is pyWGCNA_ASM1, so your code would be something like that:

pyWGCNA_ASM1 = PyWGCNA.readWGCNA("ASM.p")
pyWGCNA_ASM1.moduleTraitCor.head(5)

[bsb2014]

Here is an R method (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-03-relateModsToExt.pdf)

[nargesr]

I need it as a Python function if you want to add it to the package.