writeSigPathway          package:sigPathway          R Documentation

_W_r_i_t_e _r_e_s_u_l_t_s _o_f _p_a_t_h_w_a_y _a_n_a_l_y_s_i_s _t_o _H_T_M_L _f_o_r_m_a_t

_D_e_s_c_r_i_p_t_i_o_n:

     Writes the table of top-ranked pathways and their associated probe
     set to HTML files.

_U_s_a_g_e:

     writeSigPathway(spList, resDir = getwd(),
                     outputDirName = "sigPathway_results",
                     topIndexFileName = "TopPathwaysTable.html")
     writeSP(rpDF, gpsList, parameterList = NULL, resDir = getwd(),
             outputDirName = "sigPathway_results",
             topIndexFileName = "TopPathwaysTable.html")

_A_r_g_u_m_e_n_t_s:

  spList: a list containing the output from the 'runSigPathway'
          function

    rpDF: a data frame of top-ranked pathways from 'rankPathways' or
          'rankPathways.NGSk'

 gpsList: a list containing data frames of probes represented in gene
          sets from 'getPathwayStatistics' or
          'getPathwayStatistics.NGSk'

parameterList: a list containing the values of parameters used in the
          analysis

  resDir: a character string specifying the file directory to write the
          results

outputDirName: a character string specifying the folder to write the
          results within 'resDir'

topIndexFileName: a character string specifying the name for the HTML
          file containing the table of top-ranked pathways

_D_e_t_a_i_l_s:

     These functions export the results of the pathway analysis (e.g.,
     'runSigPathway') to several HTML files.  The user can then quickly
     browse through the files for genes of interest within the
     top-ranked genes.

_V_a_l_u_e:

     None returned

_N_o_t_e:

     This function only uses the output of 'runSigPathway' to generate
     the HTML files.  Please see the help page of 'runSigPathway' for
     example usage.  The 'writeSP' function should be used for those
     who have taken calculated the pathway statistics separately as
     shown in the help file of 'calculate.NTk', 'calculate.NEk', and
     'calculate.NGSk'

_A_u_t_h_o_r(_s):

     Weil Lai

