In the result, "beta" indicates : beta coefficient, odds ratio if binary outcomes (alternative allele vs. reference
allele). However, when I conduct GWAS on binary outcomes, there are some SNPs with beta < 0. It's impossible that the odds ratio is < 0. Would you mind me asking how to interpret it? Should I delete SNPs with beta < 0?
id chr pos rs.id ref alt AF.alt mac num beta SE pval
1: 3 22 16868201 C A 0.0004218781 17 20148 0.95400134 1.41909658 0.50141843
2: 5 22 16868590 G A 0.0005707763 23 20148 -1.06041310 1.18949813 0.37267203
3: 6 22 16868603 C T 0.0003226127 13 20148 -1.06501842 1.50172130 0.47820133
4: 7 22 16868711 G A 0.0002977963 12 20148 -1.05899912 1.67452636 0.52711436
5: 12 22 16869223 G A 0.2621351995 10563 20148 -0.12863379 0.06312118 0.04156131
In the result, "beta" indicates : beta coefficient, odds ratio if binary outcomes (alternative allele vs. reference allele). However, when I conduct GWAS on binary outcomes, there are some SNPs with beta < 0. It's impossible that the odds ratio is < 0. Would you mind me asking how to interpret it? Should I delete SNPs with beta < 0?