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Univariate Analysis in Mx PowerPoint PPT Presentation

Univariate Analysis in Mx. Boulder, 2004. Group Structure. Title Type: Data/ Calculation/ Constraint Reading Data Matrices Declaration Assigning Specifications/ Values Matrix Algebra and/or Means/ Covariances Options End. Additional Commands. ! Comments #NGroups <number of groups>

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Univariate Analysis in Mx

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Univariate Analysis in Mx

Boulder, 2004

Group Structure

• Title

• Type: Data/ Calculation/ Constraint

• Reading Data

• Matrices Declaration

• Assigning Specifications/ Values

• Matrix Algebra and/or

• Means/ Covariances

• Options

• End

Additional Commands

• ! Comments

• #NGroups <number of groups>

• #define <name> <number>

e.g. #define nvar 1

• #define <\$name> <string>

• #include filename

Reading Data

• Data NInputvars=<n> [NObs=<n>]

• Rectangular File=

• Missing=

• Labels

• Select if

• Select if zyg =1;

• Select

Summarized in filename.dat

Matrices Declaration

• Begin Matrices;

• <Name> <type> <rows> <columns>

• End Matrices;

• Matrix Types: Mx manual p. 56

• Begin Matrices = Group <number>

Matrix Algebra

• Begin Algebra;

• <matrix name> = <matrix formula>;

• <matrix name> = <matrix formula>;

• End Algebra;

• Matrix Operations: Mx Manual p. 59

• Matrix Functions: Mx Manual p. 64

Means/Covariances

• Means <formula>;

e.g. Means M;

dimensions of expected matrix must equal dimensions of observed means

• Covariances <formula>;

dimensions of expected covariance matrix must equal the square of the number of variables

Mx Script I

#NGroups 2

#define nvar 1

#define nsib 2

G1: male MZ twin pairs

Data NInput_vars=5

Missing=-1.00

Rectangular File=Agg10.rec

Labels ZYG RB10A AGG10A RB10B AGG10B

Select if zyg =1 ; ! select MZM twins

Select AGG10A AGG10B ;

May be put in agg10.dat and included with #Include filename

Mx Script II

Begin Matrices;

X Symm nsib nsib Free! covariances

I Iden nsib nsib

M Full nvar nsib Free! means

End Matrices;

Start 2 X 1 1 X 2 2! starting values for variances

Start 0.5 M 1 1 M 1 2! starting values for means

Begin Algebra;

O= \sqrt(I.X)~&X;! MZM correlation

End Algebra;

Means M;! model for MZM means

Covariances X;! model for MZM (co)variances

! Interval @95 O 2 1

Option RSiduals

End

Mx Script III

Begin Matrices;

Y Symm nsib nsib Free! covariances

I Iden nsib nsib

N Full nvar nsib Free! means

End Matrices;

Start 2 Y 1 1 X 2 2! starting values for variances

Start 0.5 N 1 1 N 1 2! starting values for means

Begin Algebra;

P= \sqrt(I.Y)~&Y;! DZM correlation

End Algebra;

Means N;! model for DZM means

Covariances Y;! model for DZM (co)variances

! Interval @95 P 2 1

Option RSiduals

End

Mx Script IV

! equate means

Equate M 1 1 1 M 1 1 2 N 2 1 1 N 2 1 2

End

! equate means and variances

Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2

End

1.00 / 0.50

1.00

1.00 / 0.25

1.00

1.00

1.00

1.00

1.00

1.00

1.00

1.00

A1

C1

E1

D1

A2

C2

E2

D2

a

c

e

d

a

c

e

d

P1

P2

Univariate Mx Script I

#NGroups 3

#define nvar 1 ! define nvar as number of variables

#define nsib 2

Title G1: Model Parameters

Calculation

Begin Matrices;

X Lower nvar nvar Free! additive genetic structure

Y Lower nvar nvar Free! common environmental structure

Z Lower nvar nvar Free! unique environmental path struct.

W Lower nvar nvar Free! dominance structure

H Full 1 1! scalar fixed @ .5 for DZ cov of A

Q Full 1 1! scalar fixed @ .25 for DZ cov of D

End Matrices;

1.00 / 0.50 [H]

1.00

1.00 / 0.25 [Q]

1.00

1.00

1.00

1.00

1.00

1.00

1.00

1.00

A1

C1

E1

D1

A2

C2

E2

D2

a [X]

c [Y]

e [Z]

d [W]

a [X]

c [Y]

e [Z]

d [W]

P1

P2

Univariate Mx Script II

Matrix H .5

Matrix Q .25

Start .5 all! starting values for free parameters

Begin Algebra;

A= X*X' ;! additive genetic variance

C= Y*Y' ; ! common environmental variance

E= Z*Z' ;! unique environmental variance

D= W*W’;! dominance variance

V= A+C+E+D;! total variance

P= A|C|E|D;! put parameters in one matrix

S= P@V~;! standardized variance components

End Algebra;

Interval @95 S 1 1 – S 1 3! confidence intervals

End

Univariate Mx Script III

G2: male MZ twins, datagroup

Data NInput_vars=5

Missing=-1.00

Rectangular File= Agg10.rec

Labels ZYG RB10A AGG10A RB10B AGG10B

Select if zyg =1;! select MZM twins

Select AGG10A AGG10B ;

Begin Matrices = Group 1;

M Full nsib nvar Free! means

End Matrices;

Start 0.5 M 1 1 M 1 2! starting values for means

Means M;! model for means

Covariances! model for MZ variance/covariances

A+C+E+D| A+C+D _

A+C+D| A+C+E+D;

Options RSiduals

End

Univariate Mx Script IV

G3: male DZ twins, datagroup

Data NInput_vars=

Missing=-1.00

Rectangular File= Agg10.rec

Labels ZYG RB10A AGG10A RB10B AGG10B

Select if zyg =2;! select DZM twins

Select AGG10A AGG10B ;

Begin Matrices = Group 1;

M Full nsib nvar Free! means

End Matrices;

Start 0.5 M 1 1 M 1 2! starting values for means

Means M;! model for means

Covariances! model for DZ variance/covariances

A+C+E+D| H@A+C+Q@D _

H@A+C+Q@D| A+C+E+D;

Option RSiduals

End

Mx Script V

Save satm.mxs

! equate means

Equate M 1 1 1 M 1 1 2 N 2 1 1 N 2 1 2

End

! equate means and variances

Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2

End

Get satm.mxs

! equate variances only

Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2

End