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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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force module assignment for all genes #137

Closed Brawni closed 9 months ago

Brawni commented 10 months ago

Hello! I often time find genes of interest being assigned to no modules (ie grey module) and so i have to run multiple iterations tuning parameters at each step to try to get them to a more meaningful module. What would be the parameters that can help the most in being less strict with module assignment ? I wonder if it's legit to just assign each gene to the eigenvector to which they are most correlated? If it is, I think that would be a nice optional feature to add. Assigning genes to module would be very quick using the modules table but I'm wondering if forcing assignments make sense or not?

Thanks so much and great package!!

smorabit commented 10 months ago

Forcing all of the grey module genes into other modules is not recommended. There are many parameters that you can try to change in ConstructNetwork that will affect the downstream modules, like mergeCutHeight or detectCutHeight for example.