ccParams                package:BGmix                R Documentation

_R_e_a_d _p_o_s_t_e_r_i_o_r _m_e_a_n_s _a_n_d _c_l_a_s_s_i_f_i_c_a_t_i_o_n _p_r_o_b_a_b_i_l_i_t_i_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 posterior means from BGmix AND reads
     posterior probabilities of each gene being classified in the null
     mixture component.

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

     ccParams(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 variance parameters?

     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:

  mbeta : matrix no. genes x no. effects. Posterior means of gene
          effect parameters (usually gene means and log fold changes).

   msig2: matrix no. genes x no. variances. Posterior means of gene
          variances.

     mbb: vector of hyperparameters (b) for gene variances (posterior
          means).

     maa: vector of hyperparameters (a) for gene variances (posterior
          means).

    mtau: matrix no. genes x no. conditions. Posterior means of gene
          precisions.

    mwtc: vector of posterior mean mixture weights

     mzg: vector of posterior mean allocation for each gene

    meta: vector of mixture parameters (eta)

 mlambda: vector of mixture parameters (lambda)

      pc: matrix no. genes x no. mixture components. Posterior
          probability for each gene of being classified into each
          mixture component.

_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)
     params <- ccParams(outdir)

