summaryCopa               package:copa               R Documentation

_C_r_e_a_t_e _S_u_m_m_a_r_y _S_h_o_w_i_n_g _T_o_p _G_e_n_e _P_a_i_r_s

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

     This function can be used to output a data.frame containing the ID
     and optionally the gene symbol for the top gene pairs, based on
     the number of outliers.

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

     summaryCopa(copa, pairnum, lib = NULL)

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

    copa: An object of class 'copa', resulting from a call to the
          'copa' function. 

 pairnum: The maximum number of outlier pairs to be output. A table can
          be output first using 'tableCopa'

     lib: For Affymetrix data that have an annotation package, this can
          be specified and the table will then also contain the gene
          symbol

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

     The output from this function is a 'data.frame' with the number of
     outliers, the manufacturer identifiers, and optionally, the gene
     symbol for the genes.

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

     James W. MacDonald <jmacdon@med.umich.edu>

_R_e_f_e_r_e_n_c_e_s:

     Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS
     transcription factor genes in prostate cancer. Science. 2005 Oct
     28;310(5748):644-8.

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

     if(interactive()){
     library(Biobase)
     data(sample.ExpressionSet)
     cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
     tmp <- copa(sample.ExpressionSet, cl)
     summaryCopa(tmp, 6)
     }

