selectGeneSets          package:sigPathway          R Documentation

_S_e_l_e_c_t _g_e_n_e _s_e_t_s _t_o _b_e _a_n_a_l_y_z_e_d _i_n _p_a_t_h_w_a_y _a_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

     Selects gene sets to be analyzed in pathway analysis based on
     minimum and maximum number of probe sets to consider per pathway.

_U_s_a_g_e:

     selectGeneSets(G, probeID, minNPS = 20, maxNPS = 500)

_A_r_g_u_m_e_n_t_s:

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

 probeID: a character vector containing the names of probe sets
          associated with a matrix of expression values

  minNPS: an integer specifying the minimum number of probe sets in
          'probeID' that should be in a gene set

  maxNPS: an integer specifying the maximum number of probe sets in
          'probeID' that should be in a gene set

_D_e_t_a_i_l_s:

     This function selects the appropriate pathways from a large,
     curated list based on the minimum and maximum number of probe sets
     that should be considered in a gene set.  It creates three
     vectors: 'nprobesV' and 'indexV' representing a sparse indicator
     matrix and 'indGused' indicating which gene sets were selected
     from 'G'.

_V_a_l_u_e:

     A list containing 

nprobesV: an integer vector indicating the number of probe sets in
          'probeID' that is in each selected gene set

  indexV: an integer vector containing positions for each 1s in the
          sparse indicator matrix

indGused: an integer vector indicating which pathways in 'G' were
          chosen

_N_o_t_e:

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

_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>

