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

