!
! Finnish families containing probands suffering from neuronal ceroid
! lipofuscinosis described in Savukoski et al AJHG 1994; 55: 695-701.
! Linkage disequilibrium mapping using 3 chromosome 13 loci
!
! D13S162 D13S160 D13S170
!
! 13q22-31 D13S162 -- 3cM -- D13S160 -- 3 cM -- D13S170 13q31-32
!
! Numbering of individuals runs as per Figure 1 generation by generation
! and left to right
!
include macros.in
set locus lincl aff       .     neuronal ceroid lipofuscinosis    
set locus oneperfam aff   .     choosing one case per family
set locus D13S162 mar   70.097  74874668 bp (chr 13)
set locus D13S160 mar   73.522  78076607 bp (chr 13)
set locus D13S170 mar   75.124  80007129 bp (chr 13)
read pedigree inline
1  1  x x m n n 2 4 1 5 5  9  
1  2  x x f n n 4 5 3 5 5  7  
1  3  1 2 f y y 4 4 5 5 5  5  
1  4  1 2 m y n 4 4 5 5 5  5  
1  5  1 2 f n n 4 5 3 5 5  7  
1  6  1 2 f n n 2 4 1 3 7  9  
1  7  1 2 f n n 2 4 1 3 7  9  
2  1  x x m n n 4 8 2 5 3  5  
2  2  x x f n n 4 6 4 5 1  5  
2  3  1 2 m n n 6 8 2 4 1  3  
2  4  1 2 m n n 4 6 4 5 5  5  
2  5  1 2 f n n 6 8 2 4 1  3  
2  6  1 2 m n n 4 8 2 5 3  5  
2  7  1 2 m y y 4 4 5 5 5  5  
2  8  1 2 m y n 4 4 5 5 5  5  
2  9  1 2 f n n 4 8 2 5 3  5  
3  1  x x m n n x x x x x  x  
3  2  x x f n n x x x x x  x  
3  3  x x f n n 4 7 4 5 5  8  
3  4  1 2 m n n 4 7 4 5 5  6  
3  5  1 2 m n n 4 7 4 5 5  8  
3  6  x x f n n 3 4 4 5 5  7  
3  7  4 3 f n n 4 7 4 4 6  8  
3  8  4 3 f n n 4 7 4 4 6  8  
3  9  4 3 m y y 4 4 4 5 5  6  
3  10 5 6 m n n 4 7 4 5 5  8  
3  11 5 6 m y n 4 4 5 5 5  5  
4  1  x x m n n 4 8 3 5 5  8  
4  2  x x f n n 1 4 1 5 2  4  
4  3  1 2 m y y 4 4 5 5 2  5  
4  4  1 2 m n n 4 8 3 5 2  8  
5  1  x x m n n 4 5 1 5 6  10 
5  2  x x f n n 4 5 1 6 4  10 
5  3  1 2 f n n 4 4 1 1 10 10 
5  4  1 2 m n n 4 5 5 6 4  6  
5  5  1 2 f n n 4 4 1 5 6  10 
6  1  x x m n n 4 5 1 4 3  11 
6  2  x x f n n 4 4 2 5 3  10 
6  3  1 2 m y y 4 4 1 5 3  3  
6  4  1 2 m n n 4 4 1 2 3  10 
7  1  x x m n n 3 4 5 6 3  7  
7  2  x x f n n 4 6 2 5 4  7  
7  3  1 2 f n n 4 4 5 5 7  7  
7  4  1 2 f n n 4 6 2 5 4  7  
8  1  x x m n n x x x x x  x  
8  2  x x f n n 2 4 3 5 2  5  
8  3  1 2 f n n 2 4 3 5 2  5  
8  4  1 2 f y y 4 4 5 5 5  5  
8  5  1 2 m n n 1 4 1 5 5  8  
9  1  x x m n n 1 4 1 5 2  5  
9  2  x x f n n 4 7 2 5 5  5  
9  3  1 2 m n n 1 7 1 5 5  5  
9  4  1 2 f y y 4 7 5 5 2  5  
10 1  x x m n n 2 5 4 5 5  7  
10 2  x x f n n 4 7 2 5 5  7  
10 3  1 2 f n n 4 5 4 5 5  7  
10 4  1 2 f y y 2 4 5 5 5  5  
11 1  x x m n n 4 4 1 5 3  4  
11 2  x x f n n 2 4 5 6 4  4  
11 3  1 2 m y y 4 4 5 5 4  4  
11 4  1 2 f n n 2 4 5 6 4  4  
12 1  x x m n n 4 4 4 5 x  x  
12 2  x x f n n 3 4 1 2 x  x  
12 3  1 2 f y y 4 4 1 5 x  x  
13 1  x x m n n 4 4 3 5 x  x  
13 2  x x f n n 4 8 2 5 x  x  
13 3  1 2 m y y 4 4 5 5 x  x  
13 4  1 2 f y n 4 4 5 5 x  x  
14 1  x x m n n x x x x x  x  
14 2  x x f n n x x x x x  x  
14 3  1 2 f y y 4 4 5 5 x  x  
14 4  1 2 f n n x x x x x  x  
;;;;
run
$ echo "lincl 0.002 0.01,0.01,0.90 recessive" > lincl.model
$ echo "lincl 0.001 0.05,0.50,0.50 dominant" >> lincl.model