TRAIT variable </ options> ;

The TRAIT statement identifies the binary variable that indicates which individuals are cases and which are controls, or that represents a dichotomous trait. This variable can be character or numeric, but it must have only two nonmissing levels. When this statement is used and the original or stepwise EM algorithm is implemented to estimate haplotype frequencies, the "Test for Marker-Trait Association" table is included in the output.

There are two options you can specify in the TRAIT statement:

PERMS=number

PERMUTATION=number

specifies the number of permutations to be used to calculate the empirical -value of the haplotype case-control tests. This number must be a positive integer. By default, no permutations are used and the -value is calculated using the chi-square test statistic. Note that this option can greatly increase the computation time.

TESTALL

specifies that each individual haplotype should be tested for association with the TRAIT variable. When this option is included in the TRAIT statement, the "Tests for Haplotype-Trait Association" table is included in the output.