I have a set of RNA-seq data for 2000 samples with multiple obesity-trait indicators (e.g., BMI, Waist-to-hip ratio, etc). I know WGCNA can handle numeric, ordinal, or binary traits. I wondering if I could include all these obesity-trait indicators into the WGCNA analysis all at once or not, because no single indicator is perfect. In addition, I want to keep my indicators as continuous variables to avoid information loss.
So, my questions is: Can WGCNA handle multiple traits/indicators at once in an analysis? Or, do you recommend that I run each indicators in a separate WGCNA?
Another questions: these indicators are somewhat dependent. I am wondering if I can still do the consensus WGCNA to find common modules across these indicators if I run each indicators separately or not.
Thank you in advance!