Question: How To Calculate The Genomic Inflation Factor From The Plink Output?
1
gravatar for Liyf
6.6 years ago by
Liyf30
Liyf30 wrote:

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 • 3.4k views
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Liyf30
1
gravatar for Maxime Lamontagne
6.6 years ago by
Québec
Maxime Lamontagne2.1k wrote:

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 COMMENTlink written 6.6 years ago by Maxime Lamontagne2.1k
1
gravatar for Liyf
6.6 years ago by
Liyf30
Liyf30 wrote:

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

ADD COMMENTlink written 6.6 years ago by Liyf30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1825 users visited in the last hour