********** pedgenie 2.6 Report **********
Created: Fri May 09 16:12:13 MDT 2008
Specification from: TDT.rgen
Data from: PhasedPedigree.dat
Runtime global parameters: 
  alleleformat=numeric
  ccstat1=TrioTDT
  ccstat2=SibTDT
  ccstat3=CombTDT
  ccstat4=Quantitative
  covar1=1
  distribution=simulation
  drop=DropSim
  dumper=TDTDumper
  locus 1=SNP1
  locus 2=SNP2
  missingdata=0
  nsims=20
  report=report
  rseed=777
  top=AlleleFreqTopSim
  top-sample=all

________________________________________________________________________________ 
** Analysis 1 **   Loci : SNP1    Model : Additive   Type : genotype

** Study : study1

============================== Trio TDT Table ==============================

Parents GenoTyp ---------------------- Case's GenoType ----------------------
                             mm             mM             MM          TOTAL

mm x mm        :              0              0              0              0
mm x mM        :              0             16              0             16
mm x MM        :              0              0              0              0
mM x mM        :              0              0              0              0
mM x MM        :              0              0             16             16
MM x MM        :              0              0              0              0
--
TOTAL          :              0             16             16             32
(# case trios analyzed / total # case trios in dataset : 32 / 32)


============================ Combined TDT Table ============================

Trio/Sib        --------------------- Overall Statistics ---------------------
                           Mean       Variance     #M frm Aff          TOTAL

Trio           :             16              8             32               
Sib            :              0              0              0               
--
TOTAL          :             16              8             32               


============================ 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


Case Parents Trio TDT (Chi-Squared Distribution) : 20 / 20 total statistics calculated
   Observed statistic : 32
   Empirical p-Value : 0
Sib TDT - Two Tailed Test : 20 / 20 total statistics calculated
   Observed statistic : 5.480078(mean : 32, variance : 8, #M from Affected : 48)
   Empirical p-Value : 0
Combined TDT - Two Tailed Test (normal distribution) : 20 / 20 total statistics calculated
   Observed statistic : 5.656854
   Empirical p-Value : 0
Quantitative, Two Tailed Test : 20 / 20, 20 / 20 total statistics calculated
   Observed statistic : 2v1:0.083453 3v1:-0.043546
   Observed Overall Statistic : 0.008663
   Empirical p-Value : 2v1:0.95 3v1:1
   Empirical Overall p-value :  :  1

________________________________________________________________________________ 
** Analysis 2 **   Loci : SNP2    Model : Additive   Type : genotype

** Study : study1

============================== Trio TDT Table ==============================

Parents GenoTyp ---------------------- Case's GenoType ----------------------
                             mm             mM             MM          TOTAL

mm x mm        :              0              0              0              0
mm x mM        :              0             16              0             16
mm x MM        :              0             16              0             16
mM x mM        :              0              0              0              0
mM x MM        :              0              0              0              0
MM x MM        :              0              0              0              0
--
TOTAL          :              0             32              0             32
(# case trios analyzed / total # case trios in dataset : 32 / 32)


============================ Combined TDT Table ============================

Trio/Sib        --------------------- Overall Statistics ---------------------
                           Mean       Variance     #M frm Aff          TOTAL

Trio           :              8              4             16               
Sib            :              0              0              0               
--
TOTAL          :              8              4             16               


============================ 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


Case Parents Trio TDT (Chi-Squared Distribution) : 20 / 20 total statistics calculated
   Observed statistic : 16
   Empirical p-Value : 0
Sib TDT - Two Tailed Test : 20 / 20 total statistics calculated
   Observed statistic : 3.75(mean : 8, variance : 4, #M from Affected : 16)
   Empirical p-Value : 0
Combined TDT - Two Tailed Test (normal distribution) : 20 / 20 total statistics calculated
   Observed statistic : 4
   Empirical p-Value : 0
Quantitative, Two Tailed Test : 20 / 20, 20 / 20 total statistics calculated
   Observed statistic : 2v1:-0.134405 3v1:0.796096
   Observed Overall Statistic : 0.451553
   Empirical p-Value : 2v1:0.95 3v1:0.55
   Empirical Overall p-value :  :  0.75

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