ccSummary               package:BGmix               R Documentation

_R_e_a_d _s_u_m_m_a_r_y _o_f _B_G_m_i_x _o_u_t_p_u_t

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

     Reads the summary.txt file output by BGmix, containing information
     about data sets used and model options. This function is called by
     ccParams, ccTrace and ccPred, therefore users will not in general
     need to call it directly.

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

     ccSummary(filedir)

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

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

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

     A list of scalar values, as follows: 

ngenes,nconds,neffects,ncomps,ntau: nos. genes, conditions, effects,
          mixture components, gene variances

  jstar : label of effect with mixture prior (labels start at 0)

move.choice.bz,move.choice.cut,move.choice.aa,
move.choice.eta,move.choice.lam,move.choice.tau,
like.choice,trace.out,trace.pred: 
          model choice options (see 'BGmix' help for details

lambda.up.init,lambda.down.init,
eta.up.init,eta.down.init
: inital
          values for eta and lambda (parameters of mixture components)

_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)
     summ <- ccSummary(outdir)

