ccTrace                package:BGmix                R Documentation

_R_e_a_d _t_r_a_c_e _f_i_l_e_s _f_r_o_m _B_G_m_i_x

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

     Reads output files containing whole posterior distributions from
     BGmix. Also calls 'ccSummary', and outputs model options.

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

     ccTrace(filedir, q.beta = T, q.sig = T, q.z = T, quiet = T)

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

 filedir: character. The name of the output directory created by BGmix.

  q.beta: logical. Read beta values?

   q.sig: logical. Read gene variances?

     q.z: logical. Read z values?

   quiet: logical. Parameter passed to 'scan'. (If false, 'scan' prints
          details of number of items read in.)

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

   summ : list object output by 'ccSummary'

    eta : matrix (no. components -1) x no. MCMC samples. Posterior of
          mixture component parameters (eta).

 lambda : matrix (no. components -1) x no. MCMC samples. Posterior of
          mixture component parameters (lambda).

     aa : matrix no. MCMC samples x no. variances. Posterior of
          variance hyperparameters (a).

     bb : matrix no. MCMC samples x no. variances. Posterior of
          variance hyperparameters (b).

    wtc : matrix no. MCMC samples x no. mixture components. Posterior
          of mixture weights.

   beta : matrix no. effects x no. genes x no. MCMC samples. Posterior
          of gene effects.

   sig2 : matrix no. variances x no. genes x no. MCMC samples.
          Posterior of gene variances.

     zg : matrix no. MCMC samples x no. genes. Posterior of gene
          allocations.

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

     Alex Lewin

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

     ## Note this is a very short MCMC run!
     ## For good analysis need proper burn-in period.
     data(ybar,ss)
     outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1)
     tr <- ccTrace(outdir)

