** Mx startup successful **
**MX-PC 1.46b** Job started on 03/17/00 at 13:08:40
!
! This is a univariate linkage job, courtesy of D. Boomsma, March 2000
!
! The data are from Keavney et al. (HMG, 1999) on angiotensin-
! converting enzyme (ace). This script reads in some family identifiers,
! then the probability of sharing 0, 1, or 2 alleles ibd (pibd0, pibd1, pibd2),
! followed by the first sib's genotype (a1s1,a2s1) then the second sib's
! genotype (a1s2,a2s2). Note that the ibd sharing probabilities can be obtained
! from, e.g., Mapmaker/Sibs, Genehunter or Simwalk2.
!
The following MX script lines were read for group 1
#DEFINE NVAR 1
TITLE QTL LINKAGE MODEL
DATA NGROUPS=1 NINPUT=13 NMODEL=1
MISSING=-99.989998
NOTE: Missing value *string* set to '-99.989998'
RECTANGULAR FILE=MARKER10.DAT
NOTE: Rectangular file contained 107 records with data
LABELS
LOCUS PEDNUM ID1 ID2 PIBD0 PIBD1 PIBD2 ACE1 ACE2 A1S1 A2S1 A1S2 A2S2
SELECT IF A1S1 ^= 0 ! THESE REPRESENT A POOR-MAN'S MISSING VALUE CODES
NOTE: Select if yields 105 data vectors for analysis
NOTE: Vectors contain a total of 1357 observations
SELECT IF A2S1 ^= 0 ! THE GENOTYPES ARE CODED AS 11, 12 AND 22
NOTE: Select if yields 105 data vectors for analysis
NOTE: Vectors contain a total of 1357 observations
SELECT IF A1S2 ^= 0 ! FOR MARKER ALLELES AA, AA, AND AA
NOTE: Select if yields 104 data vectors for analysis
NOTE: Vectors contain a total of 1344 observations
SELECT IF A2S2 ^= 0 !
NOTE: Select if yields 104 data vectors for analysis
NOTE: Vectors contain a total of 1344 observations
SELECT PIBD0 PIBD1 PIBD2 ACE1 ACE2 /! WE DON'T NEED THE GENOTYPES FOR LINKAGE
DEFINITION PIBD0 PIBD1 PIBD2/
NOTE: Selection yields 104 data vectors for analysis
NOTE: Vectors contain a total of 512 observations
MATRICES
NOTE: Definition yields 103 data vectors for analysis
NOTE: Vectors contain a total of 200 observations
A LOWER NVAR NVAR FREE !GENETIC BACKGROUND (PLUS C, AGE, ETC)
E LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT
Q FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
K FULL 3 1 !IBD PROBABILITIES (FROM MAPMAKER/SIBS) 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
U = H@A*A' ; !BACKGROUND GENETIC COVARIANCE
W = U + P@Q*Q' ; !TOTAL GENETIC COVARIANCE
V = A*A' + Q*Q' + E*E'; !TOTAL VARIANCE
Z = A*A' | Q*Q' | E*E'; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING;
S = Z@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
Y = V|W_ !EXPECTED PHENOTYPIC MATRIX
W|V;
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 Q^2 E^2
LABELS ROW Z RAWEST
LABELS COL Z A^2 Q^2 E^2
MEANS M |M ;
COVARIANCE Y ;
MATRIX A .71 !START VALUES
MATRIX E .5
MATRIX Q .5
MATRIX M 0.0
BOUND .001 100 E 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 ACE1 ACE2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 103.000 103.000 103.000 97.000 103.000
Mean 0.352 0.431 0.216 -0.043 -0.015
Variance 0.164 0.115 0.092 1.021 1.100
Minimum 0.000 0.000 0.000 -2.026 -2.109
Maximum 1.000 1.000 1.000 3.027 2.670
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Title QTL linkage model
MATRIX A
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX E
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
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 M
This is a FULL matrix of order 1 by 1
1
1 4
MATRIX P
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Q
This is a FULL matrix of order 1 by 1
1
1 3
MATRIX S
This is a computed FULL matrix of order 1 by 3
It has no free parameters specified
MATRIX U
This is a computed FULL matrix of order 1 by 1
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 W
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Y
This is a computed FULL matrix of order 2 by 2
It has no free parameters specified
MATRIX Z
This is a computed FULL matrix of order 1 by 3
It has no free parameters specified
*** WARNING! ***
I am not sure I have found a solution that satisfies
Kuhn-Tucker conditions for a minimum.
NAG's IFAIL parameter is 1
We probably have a minimum here, but you might consider trying different
starting values. You can randomize these with TH=n on the OU line, where
n is the number of times you wish to do this.
I STRONGLY recommend BOundaries to be set if you use TH
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Title QTL linkage model
MATRIX A
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX E
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.486
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 1.000
2 0.000
3 0.000
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 -0.016
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=F*K]
1
1 0.000
MATRIX Q
This is a FULL matrix of order 1 by 1
1
1 0.905
MATRIX S
This is a computed FULL matrix of order 1 by 3
[=Z@V~]
A^2 Q^2 E^2
STANDEST 0.000 0.776 0.224
MATRIX U
This is a computed FULL matrix of order 1 by 1
[=H@A*A']
1
1 0.000
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A*A'+Q*Q'+E*E']
1
1 1.056
MATRIX W
This is a computed FULL matrix of order 1 by 1
[=U+P@Q*Q']
1
1 0.000
MATRIX Y
This is a computed FULL matrix of order 2 by 2
[=V|W_W|V]
1 2
1 1.056 0.000
2 0.000 1.056
MATRIX Z
This is a computed FULL matrix of order 1 by 3
[=A*A'|Q*Q'|E*E']
A^2 Q^2 E^2
RAWEST 0.000 0.820 0.236
Vector of OBSERVED means
ACE1 ACE2
Mean 0.000 0.000
Vector of EXPECTED means
ACE1 ACE2
Mean -0.016 -0.016
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
ACE1 ACE2
ACE1 1.056
ACE2 0.000 1.056
Function value of this group: 545.182
Where the fit function is -2 * Log-likelihood of raw data
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 4 estimated parameters and 509 Observed statistics
-2 times log-likelihood of data >>> 545.182
Degrees of freedom >>>>>>>>>>>>>>>> 505
This problem used 3.8% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.77
Execution 0: 0: 0: 8.24
TOTAL 0: 0: 0: 9.01
Total number of warnings issued: 2
______________________________________________________________________________
Multiple fit option in effect.
The following MX script lines have been read:
DROP @.0 3
END
Summary of VL file data for group 1
PIBD2 PIBD1 PIBD0 ACE1 ACE2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 103.000 103.000 103.000 97.000 103.000
Mean 0.352 0.431 0.216 -0.043 -0.015
Variance 0.164 0.115 0.092 1.021 1.100
Minimum 0.000 0.000 0.000 -2.026 -2.109
Maximum 1.000 1.000 1.000 3.027 2.670
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
Title QTL linkage model
MATRIX A
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 1
MATRIX E
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 2
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 M
This is a FULL matrix of order 1 by 1
1
1 4
MATRIX P
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Q
This is a 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 3
It has no free parameters specified
MATRIX U
This is a computed FULL matrix of order 1 by 1
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 W
This is a computed FULL matrix of order 1 by 1
It has no free parameters specified
MATRIX Y
This is a computed FULL matrix of order 2 by 2
It has no free parameters specified
MATRIX Z
This is a computed FULL matrix of order 1 by 3
It has no free parameters specified
MX PARAMETER ESTIMATES
GROUP NUMBER: 1
Title QTL linkage model
MATRIX A
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.922
MATRIX E
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.459
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 1.000
2 0.000
3 0.000
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 -0.030
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=F*K]
1
1 0.000
MATRIX Q
This is a FULL matrix of order 1 by 1
1
1 0.000
MATRIX S
This is a computed FULL matrix of order 1 by 3
[=Z@V~]
A^2 Q^2 E^2
STANDEST 0.801 0.000 0.199
MATRIX U
This is a computed FULL matrix of order 1 by 1
[=H@A*A']
1
1 0.425
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A*A'+Q*Q'+E*E']
1
1 1.061
MATRIX W
This is a computed FULL matrix of order 1 by 1
[=U+P@Q*Q']
1
1 0.425
MATRIX Y
This is a computed FULL matrix of order 2 by 2
[=V|W_W|V]
1 2
1 1.061 0.425
2 0.425 1.061
MATRIX Z
This is a computed FULL matrix of order 1 by 3
[=A*A'|Q*Q'|E*E']
A^2 Q^2 E^2
RAWEST 0.850 0.000 0.211
Vector of OBSERVED means
ACE1 ACE2
Mean 0.000 0.000
Vector of EXPECTED means
ACE1 ACE2
Mean -0.030 -0.030
(OBSERVED MATRIX is nonexistent for raw data)
EXPECTED COVARIANCE MATRIX
ACE1 ACE2
ACE1 1.061
ACE2 0.425 1.061
Function value of this group: 562.409
Where the fit function is -2 * Log-likelihood of raw data
Your model has 3 estimated parameters and 509 Observed statistics
-2 times log-likelihood of data >>> 562.409
Degrees of freedom >>>>>>>>>>>>>>>> 506
Saturated model fit* >>>>>>>>>>> 545.182
Saturated model df* >>>>>>>>>>> 505
Difference Chi-squared >>>>>>>> 17.228
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 15.228
* Saturated model statistic computed earlier in this job
This problem used 3.8% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 7.30
TOTAL 0: 0: 0: 7.30
Total number of warnings issued: 2
______________________________________________________________________________