********** hapMC - production version 2.0 Report **********
Created: Mon Oct 09 11:08:12 MDT 2006
Specification from: CompositeGenotype.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 : Dom-Dom Type : Genotype
*** Study : Testing
================= Contingency Table =================
Pheno Type ---------------- Col(wt) ----------------
1(0) 2(1) TOTAL
Case : 16 32 48
Control : 64 0 64
--
TOTAL : 80 32 112
================= Quantitative Table =================
CoVar Mean ---------------- Col(wt) ----------------
1(0) 2(1) Row Total
CoVar-0 : 2.150556 2.093448 4.244004
--
Col TOTAL : 2.150556 2.093448 4.244004
Chi-squared : 2000 / 2000 total statistics calculated
Observed statistic : 59.733333
Empirical p-value : 0
Chi-squared Trend : 2000 / 2000 total statistics calculated
Observed statistic : 59.733333
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:-0.35795
Empirical p-value : 2v1:0.7355
*** Analysis 2 *** Loci : ALL MARKERS Model : Rec-Rec Type : Genotype
*** Study : Testing
================= 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 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 : 1063 / 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 : 316 / 2000 total statistics calculated
Observed statistic : 2v1:-
Empirical p-value : 2v1:-
*** Analysis 3 *** Loci : ALL MARKERS Model : Dom-Rec Type : Genotype
*** Study : Testing
================= 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 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 : 1996 / 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 : 1939 / 2000 total statistics calculated
Observed statistic : 2v1:-
Empirical p-value : 2v1:-
*** Analysis 4 *** Loci : ALL MARKERS Model : Rec-Dom Type : Genotype
*** Study : Testing
================= 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 1.975385 4.132998
--
Col TOTAL : 2.157614 1.975385 4.132998
Chi-squared : 1999 / 2000 total statistics calculated
Observed statistic : 24.888889
Empirical p-value : 0
Chi-squared Trend : 1999 / 2000 total statistics calculated
Observed statistic : 24.888889
Empirical p-value : 0
Odds Ratios, 2-Tailed Test : 1999 / 2000 total statistics calculated
Observed statistic : 2v1:-
Empirical p-value : 2v1:0.01901
Empirical Confidence Intervals : (-, -)
Quantitative, Two Tailed Test : 1995 / 2000 total statistics calculated
Observed statistic : 2v1:-1.002694
Empirical p-value : 2v1:0.35589
Elapse Time : 0 h : 1 m : 42 s