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VCU HGEN 619 - Univariate Analysis

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1Univariate AnalysisHGEN619 class 2006Testsn Saturated modeln Equality of means¨ Is m1 = m2 ?¨ Is m1MZ = m1DZ = m2MZ = m2DZ ?n Equality of variances¨ Is v1 = v2 ?¨ Is v1MZ = v1DZ = v2MZ = v2DZ ?2Equality Testsn Main Scriptn Last Groupn ....n Option Multiple Issatn Endn Save ozbmisat.mxsn ! equate means and variancesn Equate M 1 1 1 M 1 1 2 M 2 1 1 M 2 1 2n Equate X 1 1 1 X 1 2 2 X 2 1 1 X 2 2 2n EndSpecific Equality Testsn Get ozbmisat.mxsn ! equate means within zygosity groupsn Equate M 1 1 1 M 1 1 2n Equate M 2 1 1 M 2 1 2n Endn ! equate means across zygosity groupsn Equate M 1 1 1 M 1 1 2 M 2 1 1 M 2 1 2n Endn ! equate variances within zygosity groupsn Equate X 1 1 1 X 1 2 2n Equate X 2 1 1 X 2 2 2n Endn ! equate variances across zygosity groupsn Equate X 1 1 1 X 1 2 2 X 2 1 1 X 2 2 2n End3Multiple Fit45781041010parDZ (group 2)MZ (group 1)3931134311V8981134311IVv4covv3m4m3v2covv1m2m110981154311III10986654311IIGet filename.mxs: back to 10 free parameters3931134311ISave filename.mxs: 10 free parameters10987654321FullUnivariate Genetic Analysisn Saturated Models¨ Free variances, covariances¨ Free meansn Univariate Models¨ Variances partitioned in a, c/d and e¨ Free means (or not)4ACE ModelT2AEA Ca ac eT11 111Ee1Cc11 or .51ACE Model + MeansT2AEA Ca ac eT11 111Ee1Cc11 or .511m1 or m3 m2 or m45Testsn ACE modeln Is a significant ? -> CE modeln Is c significant ? -> AE modeln Is there significant family resemblance ? -> E modeln ADE model! Estimate variance components - ACED model! OZ BMI data - younger femalesn #NGroups 4n #define nvar 1n #define nvar2 2n Title 1: Model Parametersn Calculationn Begin Matrices;n X Lower nvar nvar Free ! an Y Lower nvar nvar ! cn Z Lower nvar nvar Free ! en W Lower nvar nvar Free ! dn H Full 1 1 ! 0.5n Q Full 1 1 ! 0.25n End Matrices;n Matrix H .5n Matrix Q .25n Label Row X add_genn Label Row Y com_envn Label Row Z spec_envn Label Row W dom_genn Begin Algebra;n A= X*X'; ! a^2n C= Y*Y'; ! c^2n E= Z*Z'; ! e^2n D= W*W'; ! d^2n End Algebra;n Endozbmifyace.mx6! Estimate variance components - ACED model! OZ BMI data - younger females IIn Title 2: MZ datan #include ozbmi.datn Select if zyg =1n Select bmi1 bmi2 ;n Begin Matrices = Group 1;n M Full 1 nvar2 Freen Means M;n Covariancen A+C+E+D | A+C+D _n A+C+D | A+C+E+D;n Option RSiduals;n Endn Title 3: DZ datan #include ozbmi.datn Select if zyg =3n Select bmi1 bmi2 ;n Begin Matrices = Group 1;n M Full 1 nvar2 Freen End Matrices;n Means M;n Covariancen A+C+E+D | H@A+C+Q@D _n H@A+C+Q@D | A+C+E+D;n Option RSidualsn Endozbmifyace.mx! Estimate variance components - ACED model! OZ BMI data - younger females IIIn Title 4: Standardizationn Calculationn Begin Matrices = Group 1;n End Matrices;n Start .6 alln Start 20 M 2 1 1 - M 2 1 nvar2n Start 20 M 3 1 1 - M 3 1 nvar2n Begin Algebra;n V=A+C+E+D; ! total variancen P=A|C|E|D; ! concatenate parameter estimatesn S=P@V~; ! standardized parameter estimatesn End Algebra;n !ADE modeln Interval S 1 1 - S 1 4n Option NDecimals=4n Option Sat=4055.935,1767n Endozbmifyace.mx7! Estimate variance components - ACED model! OZ BMI data - younger females IVn Title 4: Standardizationn Calculationn Begin Matrices = Group 1;n End Matrices;n Start .6 alln Start 20 M 2 1 1 - M 2 1 2n Start 20 M 3 1 1 - M 3 1 2n Begin Algebra;n V=A+C+E+D;n P=A|C|E|D;n S=P@V~;n End Algebra;n !ADE modeln Interval S 1 1 - S 1 4n Option NDecimals=4n Option Sat=4055.935,1767n Option Multiplen Endn !AE modeln Drop W 1 1 1n Endn !ACE modeln Free Y 1 1 1n Endn !CE modeln Drop X 1 1 1n Endn !E modeln Drop Y 1 1 1n Endozbmifyaces.mxSubmodels: ozbmifyaces.mx5676710NP54343DF444444Mean NP6CovNPSatFreeDropEFreeFreeDropCEFreeFreeFreeACEDropFreeFreeAEFreeFreeFreeADEW (d)Z (e)Y (c)X (a)Matrix / Model8! Estimate variance components - ACED model! OZ BMI data - younger females IVn .....n !ADE modeln Interval S 1 1 - S 1 4n Option NDecimals=4n Option Sat=4055.935,1767n Option Multiplen Endn !Save ozbmify.mxsn Option Issatn Endn !AE modeln Drop W 1 1 1n Endn !ACE modeln Free Y 1 1 1n Option Sat=4055.935,1767n Endn Option Issatn Endn !CE modeln Drop X 1 1 1n Endn !E modeln Drop Y 1 1 1n Endozbmifyaces2.mxSubmodels: ozbmifyaces2.mx7 &7 &10#7 $10#Sat5676710NP21313DF444444Mean NP6CovNPSat #FreeDropEFreeFreeDropCEFreeFreeFreeACE &DropFreeFreeAEFreeFreeFreeADE $W (d)Z (e)Y (c)X (a)Matrix / Model9Goodness-of-FitAICp p25E14CE3ACE14AE3ADESatdf)P2dfP2df-2LLParameter


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VCU HGEN 619 - Univariate Analysis

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