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Question: WGCNA TOMType specification
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gravatar for aurora.savino
9 weeks ago by
aurora.savino0 wrote:

Hello,

I have a question regarding the TOMType parameter in WGCNA blockWiseModule function.

I am interested in distinguishing positively and negatively correlated groups of genes, therefore I set networkType = "signed". By mistake, though, I put TOMType = "unsigned". Specifically:

net = blockwiseModules(data ,power= 6, TOMType ="unsigned", corType="pearson", networkType = "signed", minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE,saveTOMs = T, verbose = 3)

I looked at the documentation but it still isn't clear to me what choosing TOMType = "unsigned" implies.
Additionally, I ran the function again changing to TOMType="signed" and the resulting modules seem to be very similar (almost all the same genes).

Is choosing NetworkType="signed" enough to retain the sign in the resulting modules?

Many thanks in advance for your help.

Aurora

 

ADD COMMENTlink modified 7 weeks ago by Lluís R300 • written 9 weeks ago by aurora.savino0
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gravatar for Lluís R
7 weeks ago by
Lluís R300
European Union
Lluís R300 wrote:

TOMType options handles how should conflicting TOMs be handled (TOM between gene A and B is +, between A and C is +, and between B and C is -), usually there are few conflicts that's why it doesn't make much of a difference.

The NetworkType option is described in the adjacency function. There it says:

for type = "unsigned", adjacency = |cor|^power; for type = "signed", adjacency = (0.5 * (1+cor) )^power; for type = "signed hybrid", adjacency = cor^power if cor>0 and 0 otherwise

So if you want to keep the genes positevely correlated in the same module you should use the "signed hybrid" option.

ADD COMMENTlink written 7 weeks ago by Lluís R300
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