Question: genomic inflation factor calculation
0
gravatar for lilingjoyo
6 months ago by
lilingjoyo10
Japan
lilingjoyo10 wrote:

hallo, everyone.

I'm new to GWAS data analysis. When I do QQ plot for my association analysis result produced by snptest software. The observed p-value is deviated from expected p-value. But the inflation factor lambda is quite small, it's only 1.03. How to explain this phenomenon. Followings are my codes.

chisq = qchisq(gwas$PVAL,1,lower.tail=FALSE);
lambda <- median(chisq) / qchisq(0.5,1)
inflation factor qq plot gwas • 500 views
ADD COMMENTlink written 6 months ago by lilingjoyo10
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: 1290 users visited in the last hour