! covariance structure for 4 sib-pairs - prog modified 03/03/03 ! to form basic script for QTL scans ! of sib pairs ! No QTL estimated to generate submodel fit ! global dimensions #define nvar 1 #define nsib 4 #NGroups 2 Title QTL model two group - DZ's Calculation Begin Matrices; ! residual familial and non specific environmental variance F Lower nvar nvar Free ! background A and/or C - residual Familial E Lower nvar nvar Free ! random environment Q Full nvar 1 Fixed ! qtl effect M Full 1 1 Free ! mean I Iden nsib nsib U unit nsib nsib End Matrices; start 3 all start 0 Q 1 1 1 !Start 0 M 2 1 1 Begin algebra; R = I@(E*E') + U@(F*F') ; End Algebra; End group Title QTL model two group DZ's Data NInput=12 NModel=1 RECTANGULAR FILE=sibship4.dat ! READ IN IBD WEIGHTS FOR THE 36 SIBSHIP TYPES Labels famid position p1 p2 p3 p4 pihat12 pihat13 pihat14 pihat23 pihat24 pihat34 Select if position = $repeat_number Select p1 p2 p3 p4 pihat12 pihat13 pihat14 pihat23 pihat24 pihat34 ; Definition pihat12 pihat13 pihat14 pihat23 pihat24 pihat34 ; Begin Matrices = Group 1; N Unit 1 nsib P Stan nsib nsib End Matrices; Specify P pihat12 pihat13 pihat23 pihat14 pihat24 pihat34 Means N@M; Covariance R + P@(Q*Q'); Option Rsiduals issub Exit