! Correlations for this CpG site

! Methylation variation at IGF2 locus
! Adolescent twins (Dorret)

G1: calculation group
 Data Calc NGroups=3
  Begin matrices;
    X dia 2 2 Free			!  (standard deviation) MZ
    Y stand 2 2 Free		!  correlation MZ
    S dia 2 2 Free			!  (standard deviation) DZ
    T stand 2 2 Free		!  correlation DZ

     G Full 1 1  free		! grand mean phenotypes (equal MZ - DZ)
     P full  1 1 free 		! estimated regression effects of the SNP
  End matrices;

eq S 1 1 S 2 2
eq X 1 1 X 2 2

 st .7 X 1 1 1 X 1 2 2  S 1 1 1  S 1 2 2		! provide starting values
 st .4 Y 1 2 1 T 1 2 1
 st 3.0 G 1 1 1 
 st 0.01 P 1 1 1
End

G2: MZ twins, datagroup
 Data NInput_vars= 9								! nr of inputvars per family
 Missing=-9.00									! missing values = -9.00
 REctangular file=mx_igf2_aug08_mp2_noMis.dat	! read in raw datafile, must be in same directory (no missing data for SNP)

 LABELS  family zyg age sex sex_2 IGF2_RS1004446.1 IGF2_RS1004446.2  mp2 mp2_2	! tell Mx what is found in the datafile
  
Select if  zyg = 1 ; 											! Select MZs
Select IGF2_RS1004446.1   IGF2_RS1004446.2  mp2 mp2_2 ;	! def vars and CpG site analysed = Promoter CpG2
definition IGF2_RS1004446.1 IGF2_RS1004446.2 ;

Matrices = group 1 
    V Full 1 1 fix			! observed SNP
    W Full 1 1 fix
 end matrices;

Specify V  IGF2_RS1004446.1 ;
Specify W IGF2_RS1004446.2 ;

     Means G+V*P | G+W*P ;		! means model 
     Covariances X*Y*X' ;			! model for MZ variance/covariances
End

G3: DZ twins, datagroup
 Data NInput_vars= 9								! nr of inputvars per family
 Missing=-9.00									! missing values 
  REctangular file=mx_igf2_aug08_mp2_noMis.dat	! read in raw datafile, must be in same directory

 LABELS  family zyg age sex sex_2 IGF2_RS1004446.1 IGF2_RS1004446.2  mp2 mp2_2
  
Select if  zyg = 2 ; 
Select IGF2_RS1004446.1   IGF2_RS1004446.2  mp2 mp2_2 ;	! def vars and CpG site analysed = Promoter CpG2
definition IGF2_RS1004446.1 IGF2_RS1004446.2 ;

Matrices = group 1 
    V Full 1 1 fix			! observed SNP
    W Full 1 1 fix
 end matrices;

Specify V   IGF2_RS1004446.1 ;
Specify W IGF2_RS1004446.2 ;

     Means G+V*P | G+W*P ;		! means model 
     Covariances  S*T*S';			! model for DZ variance/covariances
End