Haplotype Estimation Method

indicates whether haplotype frequencies should not be used, haplotype frequencies should be estimated, or observed haplotype frequencies in the data should be used. This option affects all linkage disequilibrium tests and measures. By default or when HAPLO=NONE or NONEHWD is specified, the composite linkage disequilibrium (CLD) coefficient is used in place of the usual linkage disequilibrium (LD) coefficient. In addition, the composite haplotype frequencies are used to form the linkage disequilibrium measures indicated by the options CORRCOEFF and DPRIME. When HAPLO=EST, the maximum likelihood estimates of the haplotype frequencies are used to calculate the LD test statistic as well as the LD measures. The HAPLO=GIVEN option indicates that the haplotypes have been observed, and thus the observed haplotype frequencies are used in the LD test statistic and measures.

Use this parameter to select the method of haplotype estimation.

Available methods are described in the table below:

Select:	Description:
EST	Uses maximum likelihood estimate of the haplotype frequency to calculate the LD test statistic and LD measures. This method is selected by default.
NONE	Uses the composite linkage disequilibrium coefficient in calculations for estimating haplotype frequencies, with test statistics and LD measures assuming Hardy-Weinberg equilibrium
NONEHWD	Uses the composite linkage disequilibrium coefficient in calculations for estimating haplotype frequencies, with test statistics and LD measures adjusting for Hardy-Weinberg disequilibrium.
GIVEN	Assumes that the haplotypes are known and are designated by the order of the alleles and so the observed haplotype frequencies are used.

To Specify an Estimation Method:

Make a selection using the drop-down menu.