!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 ______________________________________________________________________________