!David Evans & Nick Martin platelet data
! QTL linkage study of platelet count at age 14, marker 6
!Using MZ and DZ twins
The following MX script lines were read for group 1
#DEFINE NVAR 1
#DEFINE NSIB 2 ! NUMBER OF SIBLINGS
G1: MONOZYGOTIC TWINS
DATA NGROUPS=2 NINPUT=13
RECTANGULAR FILE = MARKER6
Rectangular continuous data read initiated
NOTE: Rectangular file contained 519 records with data
that contained a total of 5624 observations
LABELS
FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23
SELECT IF ZYGOSITY < 3 /
NOTE: Select if yields 287 data vectors for analysis
NOTE: Vectors contain a total of 2962 observations
SELECT PIBD0 PIBD1 PIBD2 PLT2 PLT22 /
DEFINITION PIBD0 PIBD1 PIBD2 /
NOTE: Selection yields 287 data vectors for analysis
NOTE: Vectors contain a total of 1146 observations
NOTE: Definition yields 145 data vectors for analysis
NOTE: Vectors contain a total of 285 observations
BEGIN MATRICES
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND
Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT
L FULL NVAR 1 FREE !QTL EFFECT
M FULL NVAR 1 FREE !MEANS
END MATRICES
BEGIN ALGEBRA;
A = X*X'; !ADDITIVE GENETIC VARIANCE
C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE
E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q = L*L'; !VARIANCE DUE TO QTL
V = A + Q + C + E; !TOTAL VARIANCE
T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING;
S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 Q^2 C^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 Q^2 D^2 E^2
MEANS M_M ;
COVARIANCE A+C+Q+E|A+C+Q_
A+C+Q|A+C+Q+E;
END;
The following MX script lines were read for group 2
G2: DIZYGOTIC TWINS
DATA NGROUPS=2 NINPUT=13
RECTANGULAR FILE = MARKER6
Rectangular continuous data read initiated
NOTE: Rectangular file contained 519 records with data
that contained a total of 5624 observations
LABELS
FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23
SELECT IF ZYGOSITY > 2 /
NOTE: Select if yields 232 data vectors for analysis
NOTE: Vectors contain a total of 2662 observations
SELECT PIBD0 PIBD1 PIBD2 PLT2 PLT22 /
DEFINITION PIBD0 PIBD1 PIBD2 /
NOTE: Selection yields 232 data vectors for analysis
NOTE: Vectors contain a total of 1106 observations
Note: Global variable previously defined. Updating PIBD0
Note: Global variable previously defined. Updating PIBD1
Note: Global variable previously defined. Updating PIBD2
NOTE: Definition yields 206 data vectors for analysis
NOTE: Vectors contain a total of 410 observations
BEGIN MATRICES = GROUP 1
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE
F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT
H FULL 1 1
END MATRICES
MATRIX F 0. 0.5 1.0
MATRIX H .5
SPECIFY K PIBD0 PIBD1 PIBD2;
BEGIN ALGEBRA;
P = F*K; !ESTIMATE OF PI HAT
END ALGEBRA;
MEANS M_M ;
COVARIANCE A+C+Q+E|H@A+C+P@Q_
H@A+C+P@Q|A+C+Q+E;
ST 10 X 1 1 1 !START VALUES
ST 10 Y 1 1 1
ST 10 Z 1 1 1
ST 10 L 1 1 1
ST 285 M 1 1 1
OPTION RS ND=3
OPTION IT=5000
OPTION MULTIPLE
OPTION ISSAT
END
Summary of VL file data for group 1
PIBD2 PIBD1 PIBD0 PLT2 PLT22
Code -3.000 -2.000 -1.000 1.000 2.000
Number 145.000 145.000 145.000 145.000 140.000
Mean 1.000 0.000 0.000 2.696 2.711
Variance 0.000 0.000 0.000 0.356 0.307
Minimum 1.000 0.000 0.000 1.150 1.220
Maximum 1.000 0.000 0.000 4.360 4.280
Summary of VL file data for group 2
PIBD2 PIBD1 PIBD0 PLT2 PLT22
Code -3.000 -2.000 -1.000 1.000 2.000
Number 206.000 206.000 206.000 205.000 205.000
Mean 0.256 0.475 0.269 2.671 2.634
Variance 0.138 0.136 0.129 0.297 0.357
Minimum 0.000 0.000 0.000 1.310 1.380
Maximum 1.000 1.000 1.000 4.350 4.780
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Monozygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX C
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 4
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 5
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX S
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX T
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX V
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 3
GROUP NUMBER: 2
G2: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX C
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX F
This is a FULL matrix of order 1 by 3
It has no free parameters specified
MATRIX H
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 -1
2 -2
3 -3
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 4
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 5
MATRIX P
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX S
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX T
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX V
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 3
Mx starting optimization; number of parameters = 5
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
G1: Monozygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.097
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.032
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.065
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.368
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 2.676
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.135
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 Q^2 C^2 E^2
STANDEST 0.294 0.411 0.097 0.198
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|Q|C|E]
A^2 Q^2 D^2 E^2
UNSTANDEST 0.097 0.135 0.032 0.065
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+Q+C+E]
1
1 0.330
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.311
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.179
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.255
GROUP NUMBER: 2
G2: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.097
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.032
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.065
MATRIX F
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.001
2 0.184
3 0.814
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.368
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 2.676
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=F*K]
1
1 0.906
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.135
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 Q^2 C^2 E^2
STANDEST 0.294 0.411 0.097 0.198
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|Q|C|E]
A^2 Q^2 D^2 E^2
UNSTANDEST 0.097 0.135 0.032 0.065
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+Q+C+E]
1
1 0.330
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.311
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.179
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.255
Vector of OBSERVED means
PLT2 PLT22
Mean 2.671 2.634
Vector of EXPECTED means
PLT2 PLT22
Mean 2.676 2.676
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
PLT2 PLT22
PLT2 0.330
PLT22 0.203 0.330
Function value of this group: 654.683
Where the fit function is -2 * Log-likelihood of raw data
Your model has 5 estimated parameters and 695 Observed statistics
-2 times log-likelihood of data >>> 1003.858
Degrees of freedom >>>>>>>>>>>>>>>> 690
This problem used 1.3% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 4.90
Execution 0: 0: 0:-1.22
TOTAL 0: 0: 0: 3.68
Total number of warnings issued: 0
______________________________________________________________________________
Multiple fit option in effect.
The following MX script lines have been read:
DROP @.0 L 1 1 1
END
Summary of VL file data for group 1
PIBD2 PIBD1 PIBD0 PLT2 PLT22
Code -3.000 -2.000 -1.000 1.000 2.000
Number 145.000 145.000 145.000 145.000 140.000
Mean 1.000 0.000 0.000 2.696 2.711
Variance 0.000 0.000 0.000 0.356 0.307
Minimum 1.000 0.000 0.000 1.150 1.220
Maximum 1.000 0.000 0.000 4.360 4.280
Summary of VL file data for group 2
PIBD2 PIBD1 PIBD0 PLT2 PLT22
Code -3.000 -2.000 -1.000 1.000 2.000
Number 206.000 206.000 206.000 205.000 205.000
Mean 0.256 0.475 0.269 2.671 2.634
Variance 0.138 0.136 0.129 0.297 0.357
Minimum 0.000 0.000 0.000 1.310 1.380
Maximum 1.000 1.000 1.000 4.350 4.780
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Monozygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX C
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX L
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 5
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX S
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX T
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX V
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 3
GROUP NUMBER: 2
G2: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX C
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX E
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX F
This is a FULL matrix of order 1 by 3
It has no free parameters specified
MATRIX H
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 -1
2 -2
3 -3
MATRIX L
This is a FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 5
MATRIX P
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Q
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX S
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX T
This is a computed FULL matrix of order 1 by 4
It has no free parameters specified
MATRIX V
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 3
Mx starting optimization; number of parameters = 4
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
G1: Monozygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.237
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.028
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.065
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.000
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 2.673
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.000
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 Q^2 C^2 E^2
STANDEST 0.719 0.000 0.084 0.197
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|Q|C|E]
A^2 Q^2 D^2 E^2
UNSTANDEST 0.237 0.000 0.028 0.065
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+Q+C+E]
1
1 0.330
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.487
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.166
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.255
GROUP NUMBER: 2
G2: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.237
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.028
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.065
MATRIX F
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.001
2 0.184
3 0.814
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.000
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 2.673
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=F*K]
1
1 0.906
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.000
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 Q^2 C^2 E^2
STANDEST 0.719 0.000 0.084 0.197
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|Q|C|E]
A^2 Q^2 D^2 E^2
UNSTANDEST 0.237 0.000 0.028 0.065
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+Q+C+E]
1
1 0.330
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.487
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.166
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.255
Vector of OBSERVED means
PLT2 PLT22
Mean 2.671 2.634
Vector of EXPECTED means
PLT2 PLT22
Mean 2.673 2.673
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
PLT2 PLT22
PLT2 0.330
PLT22 0.146 0.330
Function value of this group: 662.862
Where the fit function is -2 * Log-likelihood of raw data
Your model has 4 estimated parameters and 695 Observed statistics
-2 times log-likelihood of data >>> 1012.121
Degrees of freedom >>>>>>>>>>>>>>>> 691
Saturated model fit* >>>>>>>>>>> 1003.858
Saturated model df* >>>>>>>>>>> 690
Difference Chi-squared >>>>>>>> 8.263
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.004
Akaike's Information Criterion > 6.263
* Saturated model statistic computed earlier in this job
This problem used 1.3% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.52
TOTAL 0: 0: 0: 0.52
Total number of warnings issued: 0
______________________________________________________________________________