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 [email protected] 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
