rankPathways.NGSk         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 _O_n_e _o_f _t_h_e _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 one of the pathway analyses (i.e.,
     'calculate.NTk', 'calculate.NEk', 'calculate.NGSk', or
     'calculate.GSEA')

_U_s_a_g_e:

     rankPathways.NGSk(res.NGSk, G, gsList, methodName = "NGSk",
                       npath = 25)

_A_r_g_u_m_e_n_t_s:

res.NGSk: a list from the output of 'calculate.NGSk', 'calculate.NTk',
          'calculate.NEk', or 'calculate.GSEA'

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

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

methodName: a character vector of length 1 giving the name of the
          pathway analysis used in making 'res.NGSk'

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

_D_e_t_a_i_l_s:

     This function ranks the statistics given in 'res.NGSk' 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.NGSk''s statistics, the
     corresponding q-values, and the numerical ranks for the top gene
     sets.

_N_o_t_e:

     See the help page for 'calculate.NGSk' for example code that uses
     'rankPathways.NGSk'

_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>

