hgTests               package:ppiStats               R Documentation

_A _w_r_a_p_p_e_r _f_u_n_c_t_i_o_n _t_o _i_m_p_l_e_m_e_n_t _t_h_e _H_y_p_e_r_g_e_o_m_e_t_r_i_c _t_e_s_t,  
_H_y_p_e_r_G_T_e_s_t _f_o_u_n_d _w_i_t_h_i_n_g _t_h_e _C_a_t_e_g_o_r_y _a_n_d _G_O_s_t_a_t_s _p_a_c_k_a_g_e_s.

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes the instances of the hyperGParams and conducts
     a (conditional) test for over/under representation of some
     category under the Hypergeometric distribution.

_U_s_a_g_e:

     ppiHGTest4GO(parameter, filename, append=TRUE,
                           label = "Experiment name here",
                           typeGeneSet = "Describe the gene set here",
                           cs=50)

     ppiHGTest4PFAM(parameter, filename, append = TRUE,
                                label = "Experiment Name Here",
                                typeGeneSet = "Describe the Gene Set Here",
                                cs = 50)

_A_r_g_u_m_e_n_t_s:

parameter: An object of hyperGParams.

filename: A character vector. The name given to the .html file
          produced.

  append: A logical. If multiple tests are conducted using the same
          filename, then the  .html file will be appended if TRUE or
          over-written if FALSE.

   label: A character. The should give a description of the experiment
          used to  obtain the gene set.

typeGeneSet: A character: this character vector should adequately
          describe the gene set itself.

      cs: A numeric. This gives a cut-off for the size of the
          categories in which we  conduct the test.

_V_a_l_u_e:

     A instance of the class hyperGTest as well as an .html file.

_A_u_t_h_o_r(_s):

     T Chiang

