Question: How to prepare trait data file of categorical trait with more than two levels for WGCNA?
0
gravatar for Reza
14 months ago by
Reza0
Reza0 wrote:

Hi everyone,

I want to do WGCNA and estimate the correlation of modules with clinical traits. The clinical information includes nominal variable with more than two levels (not binary). How I can design and create clinicaltrait.txt file? I have attached a screenshot of the trait file, please have a look on it.

Thanks

https://ibb.co/61S6TZ7

enter image description here

wgcna rna-seq R • 716 views
ADD COMMENTlink modified 14 months ago by Kevin Blighe63k • written 14 months ago by Reza0
1
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

Well, you clearly already have the file if you are showing a screenshot of it. So, what is the problem in reading that file into R and using it in WGCNA?

There is an example, here: http://systemsbio.ucsd.edu/WGCNAdemo/

I posted a previous related answer, too: A: WGCNA modules and categorical traits relationship (and there are many other threads / questions out there)

Also, take a look at this: A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs

Kevin

ADD COMMENTlink modified 14 months ago • written 14 months ago by Kevin Blighe63k

Dear Kevin, I encountered a similar trouble. I hope you can have a look at my post at: How to convert the ordinal categorical trait in the WGCNA?

Thank you so much!

ADD REPLYlink written 7 months ago by Quark W0
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