getDensityMatrix             package:nem             R Documentation

_C_a_l_c_u_l_a_t_e _d_e_n_s_i_t_y _m_a_t_r_i_x _f_r_o_m _r_a_w _p-_v_a_l_u_e _m_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     Fit a 3 component BUM model to each column of a raw p-value
     matrix.

_U_s_a_g_e:

             getDensityMatrix(Porig, dirname=NULL, startab=c(0.3,10), startlam=c(0.6,0.1,0.3), tol=1e-4)

_A_r_g_u_m_e_n_t_s:

   Porig: matrix of raw p-values

 dirname: name of a directory to save histograms and QQ-plots to. If
          dirname=NULL, then the plots are made to the screen, and
          after each fit the user is asked to press a key in order to
          continue.

 startab: start values for alpha and beta parameter

startlam: start values for mixing coefficients

     tol: convergence tolerance: If the absolute likelihood ratio -1
          becomes smaller than this value, then the EM algorithm is
          supposed to be converged.

_D_e_t_a_i_l_s:

     The BUM density model consists of 3 components: $f(x) = lambda_1 +
     lambda_2*dbeta(x,alpha,1) + lambda_3*dbeta(x,1,beta)$. The mixing
     coefficients and the parameters alpha and beta are fitted together
     via an EM algorithm.

_V_a_l_u_e:

     log-density matrix of same dimensions as Porig: The log-densities
     can be interpreted as log signal-to-noise ratios. A value > 0
     means higher signal than noise, and a value < 0 a higher noise
     than signal.

_N_o_t_e:

     Note the difference to the previous package version: the
     LOG-density is returned now!

_A_u_t_h_o_r(_s):

     Holger Froehlich

