How To Calculate The Genomic Inflation Factor From The Plink Output?
2
1
Entering edit mode
9.9 years ago
Liyf ▴ 30

Hi, I have a question about genomic inflation factor(GIF).

When I use plink to do logistic association, I noticed that some SNP have NA in P, the question is when I calculate the GIF,do I need to remove these snp or set NA to 1?

Thanks!

plink • 4.9k views
ADD COMMENT
1
Entering edit mode
9.9 years ago

Actually, when you are using plink to make association test, the genomic inflation factor is calculated and can be found at the bottom of the log file. If you have NA in your output, check those SNPs. Maybe their frequency is 0 or they are monomorphic.

ADD COMMENT
1
Entering edit mode
9.9 years ago
Liyf ▴ 30

Yes. If you use --asso there will be GIF. But if you use --logistic there will be non.

ADD COMMENT

Login before adding your answer.

Traffic: 1108 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6