Association analysisThe basic association test is for a disease trait and is based on comparing allele frequencies between cases and controls (asymptotic and empirical p-values are available). Also implemented are the Cochran-Armitage trend test, dominant and recessive models and a two degree of freedom general model. The ability to compare different models by likelihood ratio test and to evaluate the significant of the most significant model by permutation are also incorporated. We also test for difference in missing genotype rates between cases and controls.

Chromosome SNP ID Allele 1 Frequency of allele 1 Allele 2 Association chi-square Empirical p-value ** Adjusted empirical p-value Odds ratio (allele 1)The empirical p-value is currently based on a method that will be more conservative if there are missing data that are unevenly distributed between cases and controls: this may help to partially control the confounding that can arise with non-random missing data.

Chromosome SNP MAF Case(11) genotype count Case(12) genotype count Case(22) genotype count Control(11) genotype count Control(12) genotype count Control(22) genotype count Cochran-Armitage trend test chi-square Standard allele-based chi-square General model 2df chi-square Dominant model chi-square Recessive model chi-square Cochran-Armitage trend test p-value Standard allele-based p-value General model 2df p-value Dominant model p-value Recessive model p-value General versus allelic test p-value General versus dominant test p-value General versus recessive test p-value Flag (0/1) indicating whether genotypic test was valid Best model (G, M, D, R, X=invalid)

plink.qassocwith fields as follows:

Col 1 : SNP name Col 2 : SNP chromosome Col 3 : # non-missing genotypes Col 4 : regression coefficient (beta) Col 5 : Var(beta) Col 6 : Regression r^2 Col 7 : Likelihood ratio test (chi-sq, 1 df) Col 8 : Likelihood ratio test p-value Col 9 : Wald statistic (chi-sq, 1 df) Col 10 : Wald statistic p-valueas well as the standard

plink.assocwhich contains the same fields as for case/control association testing, except the odds ratio columns are not defined. The primary use of this second

plink.tdt.asym plink.tdt.permThe first contains the basic transmitted/untransmitted allele counts for all markers, the chi-square statistics and asymptotic p-values. Also included is information about the parenTDT and a combined test.

SET1 rs1234 rs28384 rs29334 END SET2 rs4774 rs662662 rs77262 END ...The output for the set statistics is in the file

plink.set-associn the form:

Set name (SET) Number of SNPs in set (S<1, S<2, etc) (S) nth most associated SNP (i.e. order of inclusion) (SNP) Average chi-square for set of n SNPs (T) Empirical p-value for average chi-square (p0) Empirical p-value corrected for all tests within this set (p1) Empirical p-value corrected for all tests in all sets (p2)The