!
! Analysis of Patrick Ward's example pedigree AJHG 1993
! 3 allele marker locus with population frequencies 0.05, 0.55, 0.40
!
! the APM program gives
!  f_p  = 1           5.58313   2.88766   4.00000    6  -0.93163
!  f_p  = 1/sqrt[p]   8.20251   5.13005  13.20294    6   2.20773
!  f_p  = 1/p        12.75000  26.89169  52.72727    6   7.70911
!
! Ward (1993), incl par-off pairs in calculation gives
!  f_p  = 1/sqrt[p]  T(A)=2.516
!
! SIBPAIR gives -- one run of 1000 iterations
!  f_p  = 1           7.886      4.200      5.750   6     -1.042
!  f_p  = 1/sqrt[p]  11.745      7.193     18.629   6      2.567
!  f_p  = 1/p        18.830     59.015     73.588   6      7.128
!
set workdir d:\
set impute off
set iter 1000
set locus trait aff
set locus marker mar
read pedigree ward.ped
run
! freq
! assoc trait
set plevel 1
apm trait
apm trait ibd
