I. Proc Allele (SAS/Genetics)

II. Single SNP analysis

III. Tests for Multi-allelic Markers

IV. Haplotype tests

i. Macro %HAPPY (http://www.hsph.harvard.edu/faculty/kraft/soft.htm)

ii. Hapstat (http://www.bios.unc.edu/~lin/hapstat/)

Lab 2

Yu-Chun Jean Yenyyen@hsph.harvard.eduBldg.2 Rm. 200

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

Make sure you're modeling correct outcome

Dominant Model

Codominant Model

Additive Model

proc multtest pdata=outpeas bon hom fdr;run;

BY threshold is

.05/3.38~.015

Most General Model

Model -2 log L

Additivez1 z2 z3 / ref=z0 711.218

z0 z2 z3 / ref=z1 711.218

Dominantd1 d2 d3 / ref=d0 711.797

d0 d2 d3 / ref=d1 710.719

Additive Model and Dominant Model

%happy(indsn=yahoo, keep=a7 a8 a19 a20, style=MAR, outadd=yahadd, range=.05);

SNPs (two allele vars each)

Tells happy input format

Where should I save additive scores?

How rare is rare? Rare haplotypes are lumped in "other" category.

proc print data=origfreq;run;

Dataset containing ordered hap freqs and reference numbers

/* set up analysis data set */proc sort data=yahadd; by id;proc sort data=yahoo; by id;data UseMe; merge yahoo yahadd; by id;run;

/* do global haplotype test */proc logistic data=UseMe; model d = z2 z3;run;

/* test haplotype 2-4 specifically */proc logistic data=UseMe; model d = z2;run;

● Haplotype 11(z2) & Haplotype 01(z3)Log-Likelihood

-2167.7410

● Haplotype 11(z2)Log-Likelihood

-2168.0977

● Null modelLog-Likelihood

-2174.8674

LRT = 14.25

LRT =13.54