********** pedgenie 2.6 Report ********** Created: Fri May 09 16:05:32 MDT 2008 Specification from: SingleLocus2.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=AlleleFreqTopSim top-sample=all ________________________________________________________________________________ ** Analysis 1 ** Loci : SNP1 Model : Dom Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 4 44 48 Control : 28 36 64 -- TOTAL : 32 80 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.13/30 2.135915/71 4.265915 -- Col TOTAL : 2.13 2.135915 4.265915 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 16.858333 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:8.555556 Empirical p-Value : 2v1:0 Empirical Confidence Intervals : : (3.552972, 20.601778) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.036874 Empirical p-Value : 2v1:0.9715 ________________________________________________________________________________ ** Analysis 2 ** Loci : SNP1 Model : Rec Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 32 16 48 Control : 48 16 64 -- TOTAL : 80 32 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.138667/75 2.121154/26 4.259821 -- Col TOTAL : 2.138667 2.121154 4.259821 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 0.933333 Empirical p-Value : 0.276 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:1.5 Empirical p-Value : 2v1:0.347 Empirical Confidence Intervals : : (0.658188, 3.418478) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:-0.100212 Empirical p-Value : 2v1:0.925 ________________________________________________________________________________ ** Analysis 3 ** Loci : SNP1 Model : Additive Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) 3(2) TOTAL Case : 4 28 16 48 Control : 28 20 16 64 -- TOTAL : 32 48 32 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) 3(2) Row Total CoVar-0 : 2.13/30 2.144444/45 2.121154/26 6.395598 -- Col TOTAL : 2.13 2.144444 2.121154 6.395598 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 17.402778 Empirical p-Value : 0 Chi-squared Trend : 2000 / 2000 total statistics calculated Observed statistic : 9.1875 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000, 2000 / 2000 total statistics calculated Observed statistic : 2v1:9.8 3v1:7 Empirical p-Value : 2v1:0 3v1:0.001 Empirical Confidence Intervals : : (3.783088, 25.386667) (2.526316, 19.395833) Quantitative, Two Tailed Test : 2000 / 2000, 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.083453 3v1:-0.043546 Observed Overall Statistic : 0.008663 Empirical p-Value : 2v1:0.935 3v1:0.963 Empirical Overall p-value : : 0.9895 ________________________________________________________________________________ ** Analysis 4 ** Loci : SNP1 Model : Allele Type : allele ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 36 60 96 Control : 76 52 128 -- TOTAL : 112 112 224 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.13619/105 2.131959/97 4.268149 -- Col TOTAL : 2.13619 2.131959 4.268149 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 10.5 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:2.435897 Empirical p-Value : 2v1:0 Empirical Confidence Intervals : : (1.562224, 3.798173) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:-0.040557 Empirical p-Value : 2v1:0.9585 ________________________________________________________________________________ ** Analysis 5 ** Loci : SNP2 Model : Dom Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 0 48 48 Control : 48 16 64 -- TOTAL : 48 64 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.117955/44 2.146667/57 4.264621 -- Col TOTAL : 2.117955 2.146667 4.264621 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 63 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 0 / 2000 total statistics calculated Observed statistic : WARNING: reference cell has 0 value, **test** has not been performed. Empirical p-Value : - Empirical Confidence Intervals : : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.190415 Empirical p-Value : 2v1:0.8585 ________________________________________________________________________________ ** Analysis 6 ** Loci : SNP2 Model : Rec Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 16 16 32 Control : 64 0 64 -- TOTAL : 80 16 96 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.089167/72 2.315385/13 4.404551 -- Col TOTAL : 2.089167 2.315385 4.404551 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 38.4 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:- Empirical p-Value : 2v1:0.001 Empirical Confidence Intervals : : (-, -) Quantitative, Two Tailed Test : 1998 / 2000 total statistics calculated Observed statistic : 2v1:0.964745 Empirical p-Value : 2v1:0.373373 ________________________________________________________________________________ ** Analysis 7 ** Loci : SNP2 Model : Additive Type : genotype ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) 3(2) TOTAL Case : 0 32 16 48 Control : 48 16 0 64 -- TOTAL : 48 48 16 112 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) 3(2) Row Total CoVar-0 : 2.117955/44 2.096818/44 2.315385/13 6.530157 -- Col TOTAL : 2.117955 2.096818 2.315385 6.530157 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 68.444444 Empirical p-Value : 0 Chi-squared Trend : 2000 / 2000 total statistics calculated Observed statistic : 65.722222 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 0 / 2000 total statistics calculated Observed statistic : WARNING: reference cell has 0 value, **test** has not been performed. Empirical p-Value : - Empirical Confidence Intervals : : (-, -) Quantitative, Two Tailed Test : 2000 / 2000, 1998 / 2000 total statistics calculated Observed statistic : 2v1:-0.134405 3v1:0.796096 Observed Overall Statistic : 0.451553 Empirical p-Value : 2v1:0.902 3v1:0.472472 Empirical Overall p-value : : 0.674174 ________________________________________________________________________________ ** Analysis 8 ** Loci : SNP2 Model : Allele Type : allele ** Study : study1 ============================= Contingency Table ============================= Pheno Type -------------------------- Col(wt) -------------------------- 1(0) 2(1) TOTAL Case : 32 64 96 Control : 112 16 128 -- TOTAL : 144 80 224 ============================ Quantitative Table ============================ CoVar Mean -------------------------- Col(wt) -------------------------- 1(0) 2(1) Row Total CoVar-0 : 2.110909/132 2.178/70 4.288909 -- Col TOTAL : 2.110909 2.178 4.288909 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 70.103704 Empirical p-Value : 0 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:14 Empirical p-Value : 2v1:0 Empirical Confidence Intervals : : (8.639316, 22.686981) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.618563 Empirical p-Value : 2v1:0.569 Elapse Time : 0 h : 0 m : 3 s