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Univariate Analysis: Tests

This document discusses univariate analysis and genetic modeling. It provides examples of saturated models, ACE models, and submodels for estimating variance components. Specific models are run on BMI data from younger females, including ADE, AE, ACE, CE, and E models. Parameter estimates and goodness of fit statistics are compared between the models.

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jcgueinj
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54 views9 pages

Univariate Analysis: Tests

This document discusses univariate analysis and genetic modeling. It provides examples of saturated models, ACE models, and submodels for estimating variance components. Specific models are run on BMI data from younger females, including ADE, AE, ACE, CE, and E models. Parameter estimates and goodness of fit statistics are compared between the models.

Uploaded by

jcgueinj
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Univariate Analysis

HGEN619 class 2006

Tests
Saturated model n Equality of means
n
Is

m1 = m2 ? Is m1MZ = m1DZ = m2MZ = m2DZ ?


n

Equality of variances
Is

v1 = v2 ? Is v1MZ = v1DZ = v2MZ = v2DZ ?

Equality Tests
n n n n n n n n n n

Main Script Last Group .... Option Multiple Issat End Save ozbmisat.mxs ! equate means and variances Equate M 1 1 1 M 1 1 2 M 2 1 1 M 2 1 2 Equate X 1 1 1 X 1 2 2 X 2 1 1 X 2 2 2 End

Specific Equality Tests


n n n n n n n n n n n n n n n

Get ozbmisat.mxs ! equate means within zygosity groups Equate M 1 1 1 M 1 1 2 Equate M 2 1 1 M 2 1 2 End ! equate means across zygosity groups Equate M 1 1 1 M 1 1 2 M 2 1 1 M 2 1 2 End ! equate variances within zygosity groups Equate X 1 1 1 X 1 2 2 Equate X 2 1 1 X 2 2 2 End ! equate variances across zygosity groups Equate X 1 1 1 X 1 2 2 X 2 1 1 X 2 2 2 End

Multiple Fit
MZ (group 1) m1 Full 1 m2 2 v1 3 cov 4 v2 5 DZ (group 2) m3 6 m4 7 v3 8 cov 9 v4 10 10 10 1 6 1 1 1 3 8 8 8 3 9 9 9 9 9 3 10 10 8 3 4 10 8 7 5 4 par

Save filename.mxs: 10 free parameters I II III IV V 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 4 4 4 4 4 3 5 5 3 3 1 6 1 1 1

Get filename.mxs: back to 10 free parameters

Univariate Genetic Analysis


n

Saturated Models
Free

variances, covariances Free means


n

Univariate Models
Variances

partitioned in a, c/d and e Free means (or not)

ACE Model
1 or .5 1
1 1 1 1 1 1

A
a

C
c e

E
e

C
c a

T1

T2

ACE Model + Means


1 or .5 1
1 1 1 1 1 1

A
a

C
c e

E
e

C
c a

T1
m1 or m3 m2 or m4

T2
1

Tests
ACE model n Is a significant ? -> CE model n Is c significant ? -> AE model n Is there significant family resemblance ? -> E model
n n

ADE model

! Estimate variance components - ACED model ! OZ BMI data - younger females


n n n n n n n n n n n n n n n

#NGroups 4 #define nvar 1 #define nvar2 2 Title 1: Model Parameters Calculation Begin Matrices; X Lower nvar nvar Free ! a Y Lower nvar nvar ! c Z Lower nvar nvar Free ! e W Lower nvar nvar Free ! d H Full 1 1 ! 0.5 Q Full 1 1 ! 0.25 End Matrices; Matrix H .5 Matrix Q .25
n

n n n n n n n n n n

Label Row X add_gen Label Row Y com_env Label Row Z spec_env Label Row W dom_gen Begin Algebra; A= X*X'; C= Y*Y'; E= Z*Z'; D= W*W'; End Algebra; End

! ! ! !

a^2 c^2 e^2 d^2

ozbmifyace.mx

! Estimate variance components - ACED model ! OZ BMI data - younger females II


n n n n n n n n n n n n

Title 2: MZ data #include ozbmi.dat Select if zyg =1 Select bmi1 bmi2 ; Begin Matrices = Group 1; M Full 1 nvar2 Free Means M; Covariance A+C+E+D | A+C+D _ A+C+D | A+C+E+D; Option RSiduals; End

n n n n n n n n n n n n n

Title 3: DZ data #include ozbmi.dat Select if zyg =3 Select bmi1 bmi2 ; Begin Matrices = Group 1; M Full 1 nvar2 Free End Matrices; Means M; Covariance A+C+E+D | H@A+C+Q@D _ H@A+C+Q@D | A+C+E+D; Option RSiduals End

ozbmifyace.mx

! Estimate variance components - ACED model ! OZ BMI data - younger females III
n n n n n n n n n n n n n n n n n

Title 4: Standardization Calculation Begin Matrices = Group 1; End Matrices; Start .6 all Start 20 M 2 1 1 - M 2 1 nvar2 Start 20 M 3 1 1 - M 3 1 nvar2 Begin Algebra; V=A+C+E+D; ! total variance P=A|C|E|D; ! concatenate parameter estimates S=P@V~; ! standardized parameter estimates End Algebra; !ADE model Interval S 1 1 - S 1 4 Option NDecimals=4 Option Sat=4055.935,1767 End

ozbmifyace.mx

! Estimate variance components - ACED model ! OZ BMI data - younger females IV


n n n n n n n n n n n n n n n n n n

Title 4: Standardization Calculation Begin Matrices = Group 1; End Matrices; Start .6 all Start 20 M 2 1 1 - M 2 1 2 Start 20 M 3 1 1 - M 3 1 2 Begin Algebra; V=A+C+E+D; P=A|C|E|D; S=P@V~; End Algebra; !ADE model Interval S 1 1 - S 1 4 Option NDecimals=4 Option Sat=4055.935,1767 Option Multiple End

n n n n n n n n n n n n

!AE model Drop W 1 1 1 End !ACE model Free Y 1 1 1 End !CE model Drop X 1 1 1 End !E model Drop Y 1 1 1 End

ozbmifyaces.mx

Submodels: ozbmifyaces.mx
Matrix / X (a) Model Sat ADE AE ACE CE E Free Free Free Drop Free Free Drop Free Free Free Free Free Free Drop Y (c) Z (e) W (d) Cov NP 6 Mean NP 4 4 4 4 4 4 NP 10 7 6 7 6 5 3 4 3 4 5 DF

! Estimate variance components - ACED model ! OZ BMI data - younger females IV


n n n n n n n n n n n n n

..... !ADE model Interval S 1 1 - S 1 4 Option NDecimals=4 Option Sat=4055.935,1767 Option Multiple End !Save ozbmify.mxs Option Issat End !AE model Drop W 1 1 1 End

n n n n n n n n n n n n

!ACE model Free Y 1 1 1 Option Sat=4055.935,1767 End Option Issat End !CE model Drop X 1 1 1 End !E model Drop Y 1 1 1 End

ozbmifyaces2.mx

Submodels: ozbmifyaces2.mx
Matrix / Model Sat # ADE $ AE ACE & CE E Free Free Free Drop Free Free Drop Free Free Free Free Free Free Drop X (a) Y (c) Z (e) W (d) Cov NP 6 Mean NP NP 4 4 4 4 4 4 10 7 6 7 6 5 10# 3 7$ 1 Sat DF

10# 3 7& 7& 1 2

Goodness-of-Fit
-2LL df Sat ADE AE ACE CE E 3 4 3 4 5 1 2 1 P2 df p AIC )P2 df p

Parameter Estimates
a Sat ADE AE ACE CE E c e d a2 c2 e2 d2

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