help needed about PLINK joint test (--tests)

Question

[charlie.gaoc]

Hi guys, I'm trying to use PLINK to perform a 2-degree-of-freedom test to jointly test the main genetic effect as well as the interaction effect using the --tests flag in PLINK1.9. Does anyone know what method does PLINK use for joint test (--tests)? is it a Wald Test (can we get covariance of two variables from PLINK)? or a likelihood ratio test (can we get likelihood score from PLINK)? Thank you very much for your help!

Answer 1

[charlie.gaoc]

Just got in touch with the PLINK author. PLINK1.9 (or below) uses a Wald Test for joint analysis (--tests). Detail can be found in PLINK google user group.