mtdt                   package:gap                   R Documentation

_T_r_a_n_s_m_i_s_s_i_o_n/_d_i_s_e_q_u_i_l_i_b_r_i_u_m _t_e_s_t _o_f _a _m_u_l_t_i_a_l_l_e_l_i_c _m_a_r_k_e_r

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

     This function calculates transmission-disequilibrium statistics
     involving multiallelic marker.

     Inside the function are tril and triu used to obtain lower and
     upper triangular matrices.

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

     mtdt(x,n.sim=0)

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

       x: the data table

   n.sim: the number of simulations

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

     It returned list contains the following components: 

      SE: Spielman-Ewens Chi-square from the observed data

      ST: Stuart or score Statistic from the observed data

     pSE: the simulated p value

     sSE: standard error of the simulated p value

     pST: the simulated p value

     sST: standard error of the simulated p value

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

     Sham PC (1997) Transmission/disequilibrium tests for multiallelic
     loci.  Am. J. Hum. Genet. 61:774-778

     Spielman RS, Ewens WJ (1996) The TDT and other family-based tests
     for linkage disequilibrium and association. Am. J. Hum. Genet.
     59:983-989

     Miller MB (1997) Genomic scanning and the
     transmission/disequilibrium test:  analysis of error rates. Genet.
     Epidemiol. 14:851-856

     Zhao JH, Sham PC, Curtis D (1999) A program for the Monte Carlo
     evaluation  of significance of the extended
     transmission/disequilibrium test.  Am. J. Hum. Genet. 64:1484-1485

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

     Mike Miller, Jing Hua Zhao

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

     'bt'

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

     ## Not run: 
     # Copeman et al (1995) 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)

     # See note to bt for the score test obtained by SAS

     mtdt(x)
     ## End(Not run)

