Hello, I have 50 traits and I performed GWAS on each of them. Unfortunately, I have obtained significant SNPs above a false discovery rate (5%) for only 9 traits. Using Bedtools, I could extract the distance of all the SNPs from different genes for different traits.
Is it possible to do a Network analysis with this kind of data? Can you please give some links to the tutorial for network analysis?
As I have the effect of each SNP from all the 50 traits (irrespective of significance), is it also possible to do a network analysis using all the SNP effects for 50 traits?
I have never done a network analysis and do not have any idea. It is because a reviewer just asked me to do this analysis. And I am really struggling to get an idea of how to do that.
Any feedback is highly appreciated.