laptopTable              package:lapmix              R Documentation

_T_a_b_l_e _o_f _T_o_p _G_e_n_e_s _f_r_o_m _L_a_p_l_a_c_e _L_i_n_e_a_r _M_o_d_e_l _F_i_t

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

     Extract a table of the top-ranked genes from a Laplace mixture
     model fit.

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

     laptopTable(res, number=res$med.number, sort.by='L')

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

     res: the output from the 'lapmix.Fit' routine

  number: how many genes to pick out; if missing: number is determined
          by the median rule

 sort.by: character string specifying statistic to sort the selected
          genes by in the output data.frame.

_D_e_t_a_i_l_s:

     This function summarizes a Laplace mixture model fit object
     produced by 'lapmix.Fit' by selecting the top-ranked genes
     according to the posterior log-odds or M-values. 

     The 'sort.by' argument specifies the criterion used to select the
     top genes. Only two choices at the moment: '"M"' to sort by the
     (absolute) coefficient representing the log-fold-change, and '"L"'
     to sort by the posterior odds of differential expression under the
     Laplace mixture model.

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

     A dataframe with a row for the 'number' top genes and the
     following columns: 

       M: average log fold change

log.odds: log posterior odds that the gene is differentially expressed

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

     Yann Ruffieux

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

     #  See lapmix.Fit example

