Gene set tests statistics       package:topGO       R Documentation

_G_e_n_e _s_e_t _t_e_s_t_s _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Methods which implement and run a group test statistic for a class
     inheriting from 'groupStats' class. See Details section for a
     description of each method.

_U_s_a_g_e:

     GOFisherTest(object)
     GOKSTest(object)
     GOtTest(object)
     GOglobalTest(object)

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'groupStats' or decedent class.

_D_e_t_a_i_l_s:

     GOFisherTest: implements Fischer's exact test (based on
     contingency table) for 'groupStats' objects dealing with "counts".

     GOKSTest: implements the Kolmogorov-Smirnov test for 'groupStats'
     objects dealing with gene "scores". This test uses the 'ks.test'
     function and does not implement the running-sum-statistic test
     based on permutations. 

     GOtTest: implements the t-test for 'groupStats' objects dealing
     with gene "scores". It should be used when the gene scores are
     t-statistics or any other score following a normal distribution.

     GOglobalTest: implement Goeman's globaltest.

_V_a_l_u_e:

     All these methods return the p-value computed by the respective
     test statistic.

_A_u_t_h_o_r(_s):

     Adrian Alexa

_S_e_e _A_l_s_o:

     'groupStats-class', 'getSigGroups-methods'

