I have a question on how to connect the procedures of haplotype and phreg. Using haplotype procedure we can estimate haplotypes and their frequency. Based on example in SAS/Genetics, we can assign haplotypes for each subject, and their corresponding frequency. We know each subject may have different estimated haplotypes with different frequencies. In the example, 8 haplotypes are transposed to be 8 variables, which are modelled in logistic regression to get ORs for each haplotype (ORs for a unit change of frequency of a haplotype) . My question is: is it possible to estimate ORs for a haplotype with a common haplotype as a reference and how?
SAS example (http://support.sas.com/documentation/cdl/en/geneug/59659/HTML/default/geneug_haplotype_sect021.htm)