! ! 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. ! #define nvar 1 ! would be different for multivariate Title QTL linkage model Data NGroups=1 NInput=13 NModel=1 missing=-99.989998 Rectangular File=marker10.dat 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 select if a2s1 ^= 0 ! the genotypes are coded as 11, 12 and 22 select if a1s2 ^= 0 ! for marker alleles AA, Aa, and aa select if a2s2 ^= 0 ! SELECT pibd0 pibd1 pibd2 ace1 ace2 /! we don't need the genotypes for linkage Definition pibd0 pibd1 pibd2/ Matrices 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 Drop @.0 3 ! drop qtl effect as linkage test End