********** pedgenie 2.6 Report ********** Created: Fri May 09 16:22:48 MDT 2008 Specification from: PedGenieCompGenotype2.rgen Data from: PhasedPedigree.dat Runtime global parameters: alleleformat=numeric ccstat1=ChiSquared ccstat2=ChiSquaredTrend ccstat3=OddsRatiosWithCI ccstat4=Quantitative covar1=1 distribution=simulation drop=DropSim locus 1=SNP1 locus 2=SNP2 missingdata=0 nsims=2000 report=report rseed=777 top=HapFreqTopSim top-sample=all ________________________________________________________________________________ ** Analysis 1 ** Loci : SNP1 SNP2 Model : Dom-Dom Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 4 44 48 Control : 64 0 64 -- TOTAL : 68 44 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.134839/62 2.133077/39 4.267916 -- Col TOTAL : 2.134839 2.133077 4.267916 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 96.627451 Empirical p-Value : 0 Chi-squared Trend : 2000 / 2000 total statistics calculated Observed statistic : 96.627451 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:0 Empirical Confidence Intervals : : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:-0.011606 Empirical p-Value : 2v1:0.9945 ________________________________________________________________________________ ** Analysis 2 ** Loci : SNP1 SNP2 Model : Rec-Rec Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 48 0 48 Control : 64 0 64 -- TOTAL : 112 0 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.134158/101 0/0 2.134158 -- Col TOTAL : 2.134158 0 2.134158 Chi-squared : 0 / 2000 total statistics calculated Observed statistic : WARNING: row or column sum equals zero, **test** has not been performed. Empirical p-Value : - Chi-squared Trend : 0 / 2000 total statistics calculated Observed statistic : WARNING: row or column sum equals zero, **test** has not been performed. Empirical p-Value : - Odds Ratios, 2-Tailed Test : 1911 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:- Empirical Confidence Intervals : : (-, -) Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations Quantitative, Two Tailed Test : 1604 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:- ________________________________________________________________________________ ** Analysis 3 ** Loci : SNP1 SNP2 Model : Dom-Rec Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 36 12 48 Control : 64 0 64 -- TOTAL : 100 12 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.121648/91 2.248/10 4.369648 -- Col TOTAL : 2.121648 2.248 4.369648 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 17.92 Empirical p-Value : 0 Chi-squared Trend : 2000 / 2000 total statistics calculated Observed statistic : 17.92 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:0 Empirical Confidence Intervals : : (-, -) Quantitative, Two Tailed Test : 1999 / 2000 total statistics calculated Observed statistic : 2v1:0.453627 Empirical p-Value : 2v1:0.662331 ________________________________________________________________________________ ** Analysis 4 ** Loci : SNP1 SNP2 Model : Rec-Dom Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 32 16 48 Control : 64 0 64 -- TOTAL : 96 16 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.157614/88 1.975385/13 4.132998 -- Col TOTAL : 2.157614 1.975385 4.132998 Chi-squared : 1984 / 2000 total statistics calculated Observed statistic : 24.888889 Empirical p-Value : 0 Chi-squared Trend : 1984 / 2000 total statistics calculated Observed statistic : 24.888889 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 1984 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:0.05746 Empirical Confidence Intervals : : (0, infinite) Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations Quantitative, Two Tailed Test : 1899 / 2000 total statistics calculated Observed statistic : 2v1:-1.002694 Empirical p-Value : 2v1:0.377041 Elapse Time : 0 h : 0 m : 2 s