rankPathways           package:sigPathway           R Documentation

_S_u_m_m_a_r_i_z_e_s _T_o_p _P_a_t_h_w_a_y_s _f_r_o_m _P_a_t_h_w_a_y _A_n_a_l_y_s_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Summarizes top pathways from pathway analyses.

_U_s_a_g_e:

     rankPathways(res.A, res.B, G, tab, phenotype, gsList, ngroups,
                  methodNames = NULL, npath = 25, allpathways = FALSE)

_A_r_g_u_m_e_n_t_s:

   res.A: a list from the output of 'calculate.NTk' or 'calculate.NEk'

   res.B: a list from the output of 'calculate.NTk' or 'calculate.NEk'

       G: a list containing the source, title, and probe sets
          associated with each curated pathway

     tab: a numeric matrix of expression values, with the rows and
          columns representing probe sets and sample arrays,
          respectively

phenotype: a numeric (or character if 'ngroups' >= 2) vector indicating
          the phenotype

  gsList: a list containing three vectors from the output of the
          'selectGeneSets' function

 ngroups: an integer indicating the number of groups in the matrix

methodNames: a character vector of length 2 giving the names for
          'res.A' and 'res.B'

   npath: an integer indicating the number of top gene sets to consider
          from each statistic when ranking the top pathways

allpathways: a boolean to indicate whether to include the top 'npath'
          pathways from each statistic or just consider the top 'npath'
          pathways (sorted by the sum of ranks of both statistics) when
          generating the summary table

_D_e_t_a_i_l_s:

     This function ranks together the statistics given in 'res.A' and
     'res.B' and summarizes the top gene sets in a tabular format
     similar to Table 2 in Tian et al. (2005)

_V_a_l_u_e:

     A data frame showing the pathways' indices in 'G', gene set
     category, pathway title, set size, 'res.A''s statistics, 'res.B''s
     statistics, the corresponding q-values, and the ranks for the top
     gene sets.

_N_o_t_e:

     See the help page for 'calculate.NTk' or 'calculate.NEk' for
     example code that uses 'rankPathways'

_A_u_t_h_o_r(_s):

     Lu Tian, Peter Park, and Weil Lai

_R_e_f_e_r_e_n_c_e_s:

     Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S.,
     Park P.J. (2005)  Discovering statistically significant pathways
     in expression profiling studies.  _Proceedings of the National
     Academy of Sciences of the USA_, *102*, 13544-9.

     <URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102>

