bt                    package:gap                    R Documentation

_B_r_a_d_l_e_y-_T_e_r_r_y _m_o_d_e_l _f_o_r _c_o_n_t_i_n_g_e_n_c_y _t_a_b_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function calculates statistics under Bradley-Terry model. 

     Inside the function is a function toETDT which generates data
     required by ETDT.

_U_s_a_g_e:

     bt(x)

_A_r_g_u_m_e_n_t_s:

       x: the data table

_V_a_l_u_e:

     The returned value is a list containing: 

       y: A column of 1

   count: the frequency count/weight

  allele: the design matrix

  bt.glm: a glm.fit object

etdt.dat: a data table that can be used by ETDT

_R_e_f_e_r_e_n_c_e_s:

     Bradley RA, Terry ME (1952) Rank analysis of incomplete block
     designs I.  the method of paired comparisons. Biometrika
     39:324-345

     Sham PC, Curtis D (1995) An extended transmission/disequilibrium 
     test ({TDT}) for multi-allelic marker loci. Ann. Hum. Genet.
     59:323-336

_A_u_t_h_o_r(_s):

     Jing hua Zhao

_S_e_e _A_l_s_o:

     'mtdt'

_E_x_a_m_p_l_e_s:

     ## Not run: 
     # Copeman JB, Cucca F, Hearne CM, Cornall RJ, Reed PW, Ronningen KS, Undlien DE, Nistico L, Buzzetti R, Tosi R, et al.
     # (1995) Linkage disequilibrium mapping of a type 1 diabetes susceptibility gene (IDDM7) to chromosome 2q31-q33. 
     # Nat Genet 9: 80-5

     x <- matrix(c(0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
                   0,0, 1, 3, 0,0, 0, 2, 3, 0, 0, 0,
                   2,3,26,35, 7,0, 2,10,11, 3, 4, 1,
                   2,3,22,26, 6,2, 4, 4,10, 2, 2, 0,
                   0,1, 7,10, 2,0, 0, 2, 2, 1, 1, 0,
                   0,0, 1, 4, 0,1, 0, 1, 0, 0, 0, 0,
                   0,2, 5, 4, 1,1, 0, 0, 0, 2, 0, 0,
                   0,0, 2, 6, 1,0, 2, 0, 2, 0, 0, 0,
                   0,3, 6,19, 6,0, 0, 2, 5, 3, 0, 0,
                   0,0, 3, 1, 1,0, 0, 0, 1, 0, 0, 0,
                   0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
                   0,0, 1, 0, 0,0, 0, 0, 0, 0, 0, 0),nrow=12)

     # Bradley-Terry model, only deviance is available in R
     bt.ex<-bt(x)
     anova(bt.ex$bt.glm)
     summary(bt.ex$bt.glm)
     bt.ex$etdt.dat
     ## End(Not run)

