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Proc Allele (SAS/Genetics) Single SNP analysis Tests for Multi-allelic Markers Haplotype tests

Lab 2. Proc Allele (SAS/Genetics) Single SNP analysis Tests for Multi-allelic Markers Haplotype tests Macro %HAPPY (http://www.hsph.harvard.edu/faculty/kraft/soft.htm) Hapstat (http://www.bios.unc.edu/~lin/hapstat/). Yu-Chun Jean Yen yyen@hsph.harvard.edu Bldg.2 Rm. 200. Sample Dataset

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Proc Allele (SAS/Genetics) Single SNP analysis Tests for Multi-allelic Markers Haplotype tests

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  1. Lab 2 • Proc Allele (SAS/Genetics) • Single SNP analysis • Tests for Multi-allelic Markers • Haplotype tests • Macro %HAPPY (http://www.hsph.harvard.edu/faculty/kraft/soft.htm) • Hapstat (http://www.bios.unc.edu/~lin/hapstat/) Yu-Chun Jean Yenyyen@hsph.harvard.eduBldg.2 Rm. 200

  2. Sample Dataset Yahoo.dat: a comma delimited file Case-control with 1680 subjects, 16 SNPs

  3. Make sure you're modeling correct outcome

  4. Dominant Model

  5. Codominant Model

  6. Additive Model

  7. procmulttest pdata=outpeas bon hom fdr; run; BY threshold is .05/3.38~.015

  8. Most General Model

  9. Additive Model and Dominant Model

  10. SNPs (two allele vars each) %happy(indsn=yahoo, keep=a7 a8 a19 a20, style=MAR, outadd=yahadd, range=.05); Tells happy input format Where should I save additive scores? How rare is rare? Rare haplotypes are lumped in "other" category.

  11. procprintdata=origfreq; run; Dataset containing ordered hap freqs and reference numbers

  12. /* set up analysis data set */ procsortdata=yahadd; by id; procsortdata=yahoo; by id; data UseMe; merge yahoo yahadd; by id; run; /* do global haplotype test */ proclogisticdata=UseMe; model d = z2 z3; run; /* test haplotype 2-4 specifically */ proclogisticdata=UseMe; model d = z2; run;

  13. LRT = 14.25 LRT =13.54 • Haplotype 11(z2) & Haplotype 01(z3) Log-Likelihood -2167.7410 • Haplotype 11(z2) Log-Likelihood -2168.0977 • Null model Log-Likelihood -2174.8674

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