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