********** hapMC - production version 2.0 Report **********
Created: Mon Oct 09 11:17:17 MDT 2006
Specification from: Haplotype.rgen
Data from: ./GenotypeData.dat
Runtime global parameters:
ccstat1=ChiSquared
ccstat2=ChiSquaredTrend
ccstat3=OddsRatios
ccstat4=Quantitative
covar1=1
drop=HapMCDropSim
locus 1=SNP1
locus 2=SNP2
nsims=2000
report=report
rseed=777
top=HapMCTopSim
top-sample=all
________________________________________________________________
*** Analysis 1 *** Loci : ALL MARKERS Model : Hap 2 vs Hap 1 Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(0) 2(1) TOTAL
Case : 0 32 32
Control : 32 16 48
--
TOTAL : 32 48 80
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(0) 2(1) Row Total
CoVar-0 : 2.055484 2.197273 4.252757
--
Col TOTAL : 2.055484 2.197273 4.252757
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 35.555556
Empirical p-value : 0.0005
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 : 2v1:0.833911
Empirical p-value : 2v1:0.4115
________________________________________________________________
*** Analysis 2 *** Loci : ALL MARKERS Model : Hap 3 vs Hap 1 Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(0) 2(1) TOTAL
Case : 0 16 16
Control : 48 0 48
--
TOTAL : 48 16 64
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(0) 2(1) Row Total
CoVar-0 : 2.071087 1.975385 4.046472
--
Col TOTAL : 2.071087 1.975385 4.046472
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 64
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:-0.498144
Empirical p-value : 2v1:0.615
________________________________________________________________
*** Analysis 3 *** Loci : ALL MARKERS Model : Hap 4 vs Hap 1 Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(0) 2(1) TOTAL
Case : 0 32 32
Control : 16 48 64
--
TOTAL : 16 80 96
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(0) 2(1) Row Total
CoVar-0 : 2.103333 2.108219 4.211553
--
Col TOTAL : 2.103333 2.108219 4.211553
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 9.6
Empirical p-value : 0.002
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 : 2v1:0.024777
Empirical p-value : 2v1:0.9785
________________________________________________________________
*** Analysis 4 *** Loci : ALL MARKERS Model : Hap 2 vs rest REV Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(1) 2(0) TOTAL
Case : 32 16 48
Control : 16 48 64
--
TOTAL : 48 64 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(1) 2(0) Row Total
CoVar-0 : 2.197273 2.085439 4.282711
--
Col TOTAL : 2.197273 2.085439 4.282711
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 19.444444
Empirical p-value : 0.001
Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:6
Empirical p-value : 1v2:0
Empirical Confidence Intervals : (2.726267, 13.204868)
Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:0.749856
Empirical p-value : 1v2:0.4515
________________________________________________________________
*** Analysis 5 *** Loci : ALL MARKERS Model : Hap 3 vs rest REV Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(1) 2(0) TOTAL
Case : 16 32 48
Control : 0 64 64
--
TOTAL : 16 96 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(1) 2(0) Row Total
CoVar-0 : 1.975385 2.157614 4.132998
--
Col TOTAL : 1.975385 2.157614 4.132998
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 24.888889
Empirical p-value : 0.001
Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:-
Empirical p-value : 1v2:0.002
Empirical Confidence Intervals : (-, -)
Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:-1.002694
Empirical p-value : 1v2:0.324
________________________________________________________________
*** Analysis 6 *** Loci : ALL MARKERS Model : Hap 4 vs rest Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(1) 2(0) TOTAL
Case : 32 16 48
Control : 48 16 64
--
TOTAL : 80 32 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(1) 2(0) Row Total
CoVar-0 : 2.108219 2.201786 4.310005
--
Col TOTAL : 2.108219 2.201786 4.310005
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 0.933333
Empirical p-value : 0.35
Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:0.666667
Empirical p-value : 1v2:0.351
Empirical Confidence Intervals : (0.304403, 1.460055)
Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:-0.57367
Empirical p-value : 1v2:0.567
________________________________________________________________
*** Analysis 7 *** Loci : ALL MARKERS Model : Hap 3 Dom REV Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(1) 2(0) TOTAL
Case : 16 32 48
Control : 0 64 64
--
TOTAL : 16 96 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(1) 2(0) Row Total
CoVar-0 : 1.975385 2.157614 4.132998
--
Col TOTAL : 1.975385 2.157614 4.132998
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 24.888889
Empirical p-value : 0.001
Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:-
Empirical p-value : 1v2:0.002
Empirical Confidence Intervals : (-, -)
Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated
Observed statistic : 1v2:-1.002694
Empirical p-value : 1v2:0.324
________________________________________________________________
*** Analysis 8 *** Loci : ALL MARKERS Model : Hap 3 Rec REV Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(1) 2(0) TOTAL
Case : 0 48 48
Control : 0 64 64
--
TOTAL : 0 112 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(1) 2(0) Row Total
CoVar-0 : 0 2.134158 2.134158
--
Col TOTAL : 0 2.134158 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 : -
Odds Ratios, 2-Tailed Test : 1063 / 2000 total statistics calculated
Observed statistic : 1v2:-
Empirical p-value : 1v2:-
Empirical Confidence Intervals : (-, -)
Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations
Quantitative, Two Tailed Test : 316 / 2000 total statistics calculated
Observed statistic : 1v2:-
Empirical p-value : 1v2:-
________________________________________________________________
*** Analysis 9 *** Loci : ALL MARKERS Model : Hap3 Additive R Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(2) 2(1) 3(0) TOTAL
Case : 0 16 32 48
Control : 0 0 64 64
--
TOTAL : 0 16 96 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(2) 2(1) 3(0) Row Total
CoVar-0 : 0 1.975385 2.157614 4.132998
--
Col TOTAL : 0 1.975385 2.157614 4.132998
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 : 1063 / 2000, 2000 / 2000 total statistics calculated
Observed statistic : 1v3:- 2v3:-
Empirical p-value : 1v3:- 2v3:0.002
Empirical Confidence Intervals : (-, -) (-, -)
Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations
Quantitative, Two Tailed Test : 316 / 2000, 2000 / 2000 total statistics calculated
Observed statistic : 1v3:- 2v3:-1.002694
Observed Overall Statistic : -
Empirical p-value : 1v3:- 2v3:0.3245
Empirical Overall p-value : -
Elapse Time : 0 h : 4 m : 46 s