Programming the statistical procedures from SAS

Haplotype and Cox model

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Haplotype and Cox model

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)

Individual ID disease A_B_C A_B_c a_B_C a_B_c A_b_C A_b_c a_b_c a_b_C
1 1 0.29 0.21 0.21 0.29 0.00 0.00 0.00 0
2 1 0.27 0.23 0.00 0.00 0.23 0.27 0.00 0
3 0 0.00 0.27 0.00 0.23 0.00 0.23 0.27 0
4 1 0.50 0.50 0.00 0.00 0.00 0.00 0.00 0
5 1 0.27 0.23 0.00 0.00 0.23 0.27 0.00 0
6 0 0.27 0.23 0.00 0.00 0.23 0.27 0.00 0


Thanks in advance.
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