I am new to this area and I went through some tutorials and software on how to simulate and format my own TWAS data. However, I noticed that most software do not produce the N column in the output. I understand how we are getting CHR, BP, SNPs, allele columns and Z/p-score statistics. Please can someone explain how we get different values of N for different SNPs?
Edit: I should mention that I'm trying to generate TWAS based on .bim/.fam/.bed files