Daniel Weng,

The standard option (and default) is the basic allelic test, but if you use model option (-model option) you can choose Dominant and Recessive models

you can review the page: http://zzz.bwh.harvard.edu/plink/anal.shtml 

Section: 

"Alternate / full model association tests

It is possible to perform tests of association between a disease and a variant other than the basic allelic test (which compares frequencies of alleles in cases versus controls), by using the --model option. The tests offered here are (in addition to the basic allelic test):Cochran-Armitage trend test

Genotypic (2 df) test

Dominant gene action (1df) test

Recessive gene action (1df) test"

Kind regards

Hugo

Hi Hugo,

Thank you for your response. I know I can use model (--model) function to do different tests such as dominant, recessive, trend, and genotypic. However, I can't combine --tdt and --model together. I think --model test is just for association test. Am I right?

Best,

Daniel