gcontrol                 package:gap                 R Documentation

_g_e_n_o_m_i_c _c_o_n_t_r_o_l

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

     The Bayesian genomic control statistics with the following
     parameters,

       n          number of loci under consideration
       lambdahat  median(of the n trend statistics)/0.46
                  Prior for noncentrality parameter Ai is
                  Normal(sqrt(lambdahat)kappa,lambdahat*tau2)
       kappa      multiplier in prior above, set at 1.6 * sqrt(log(n))
       tau2       multiplier in prior above
       epsilon    prior probability a marker is associated, set at 10/n
       ngib       number of cycles for the Gibbs sampler after burn in
       burn       number of cycles for the Gibbs sampler to burn in

     Armitage's trend test along with the posterior probability that
     each marker is associated with the disorder is given. The latter
     is not a p-value but any value greater than 0.5 (pout) suggests
     association.

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

     gcontrol(data,zeta,kappa,tau2,epsilon,ngib,burn,idum)

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

    data: the data matrix

    zeta: program constant with default value 1000

   kappa: multiplier in prior for mean with default value 4

    tau2: multiplier in prior for variance with default value 1

 epsilon: prior probability of marker association with default value
          0.01

    ngib: number of Gibbs steps, with default value 500

    burn: number of burn-ins with default value 50

    idum: seed for pseudorandom number sequence

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

     The returned value is a list containing:

  deltot: the probability of being an outlier

      x2: the chi-squared statistic

       A: the A vector

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

     Devlin B, Roeder K (1999) Genomic control for association studies.
      Biometrics 55:997-1004

_N_o_t_e:

     Adapted from gcontrol by Bobby Jones and Kathryn Roeder,  use
     -Dexecutable for standalone program, function getnum in the
     original  code needs %*s to skip id string

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

     Bobby Jones, Jing Hua Zhao

_S_o_u_r_c_e:

     <URL: http://www.stat.cmu.edu>

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

     ## Not run: 
     test<-c(1,2,3,4,5,6,  1,2,1,23,1,2, 100,1,2,12,1,1, 
             1,2,3,4,5,61, 1,2,11,23,1,2, 10,11,2,12,1,11)
     test<-matrix(test,nrow=6,byrow=T)
     gcontrol(test)
     ## End(Not run)

