plotFDR                package:BGmix                R Documentation

_P_l_o_t _e_s_t_i_m_a_t_e_d _F_D_R _e_t_c. _f_o_r _B_G_m_i_x _o_u_t_p_u_t.

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

     Given a threshold on the posterior probabilities, genes are
     declared as null or differentially expressed. For any given
     threshold, the FDR (false discovery rate) and FNR (false
     non-discovery rate) can be estimated using the posterior
     probabilities. This function plots these quantities twice, once
     versus the threshold probabilities, and once versus the number of
     declared positives.

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

     plotFDR(res, ylim = NULL, q.plotfnr = F, q.plotpcut = T, q.plotnpos = T, ...)

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

     res: list object output from 'calcFDR'

    ylim: optional argument specifying limit for y-axis

q.plotfnr: Include FNR in plots?

q.plotpcut: Include the plot of error rates v. threshold on posterior
          probabilites?

q.plotnpos: Include the plot of error rates v. no. positives.

     ...: arguments passed to 'plot'

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

     No value is returned to R. Results from BGmix model are output to
     files.

_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)
     fdr <- calcFDR(params)
     par(mfrow=c(1,2))
     plotFDR(fdr)

