CoHyperGParams-class         package:PCpheno         R Documentation

_C_l_a_s_s "_C_o_H_y_p_e_r_G_P_a_r_a_m_s"

_D_e_s_c_r_i_p_t_i_o_n:

     A parameter class for representing all parameters needed for
     running the 'hyperGTest' method with multiprotein complexes.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form
     'new("CoHyperGParams",...)'.

_S_l_o_t_s:


     '_g_e_n_e_I_d_s': Object of class '"ANY"': A vector of gene identifiers. 
          Numeric and character vectors are probably the only things
          that make sense.  These are the gene ids for the selected
          gene set.

     '_u_n_i_v_e_r_s_e_G_e_n_e_I_d_s': Object of class '"ANY"': A vector of gene ids
          in the same format as 'geneIds' defining a subset of the gene
          ids on the chip that will be used as the universe for the
          hypergeometric calculation.  If this is 'NULL' or has length
          zero, then all gene ids on the chip will be used.

     '_a_n_n_o_t_a_t_i_o_n': A string giving the name of the annotation data
          package for the chip used to generate the data.

     '_c_a_t_e_o_g_r_y_S_u_b_s_e_t_I_d_s': Object of class '"ANY"': If the test method
          supports it, can be used to specify a subset of category ids
          to include in the test instead of all possible category ids.

     '_c_a_t_e_g_o_r_y_N_a_m_e': A string describing the category. Usually set
          automatically by subclasses.  For example "ScISI".

     '_p_v_a_l_u_e_C_u_t_o_f_f': The p-value to use as a cutoff for significance
          for testing methods that require it.  This value will also be
          passed on to the result instance and used for display and
          counting of significant results.  The default is 0.01.

     '_t_e_s_t_D_i_r_e_c_t_i_o_n': A string indicating whether the test should be
          for overrepresentation ('"over"') or underrepresentation
          ('"under"').

_M_e_t_h_o_d_s:


     _h_y_p_e_r_G_T_e_s_t 'signature(p = "HyperGParams")': Perform hypergeometric
          tests to assess over-representation of category ids in the
          gene set.  See the documentation for the generic function for
          details.  This method must be called with a proper subclass
          of 'HyperGParams'.

     '_g_e_n_e_I_d_s(_r)', '_g_e_n_e_I_d_s(_r) <- _v_a_l_u_e' Accessors for the gene
          identifiers that will be used as the selected gene list.

     _c_o_d_e{_a_n_n_o_t_a_t_i_o_n(_o_b_j_e_c_t)} Accessor for annotation

     '_o_n_t_o_l_o_g_y(_r)' Accessor for GO ontology.

     '_p_v_a_l_u_e_C_u_t_o_f_f(_r)', '_p_v_a_l_u_e_C_u_t_o_f_f(_r) <-         _v_a_l_u_e' Accessor for
          the p-value cutoff.  When setting, 'value' should be a
          numeric value between zero and one.

     '_t_e_s_t_D_i_r_e_c_t_i_o_n' Accessor for the test direction.  When setting,
          'value' must be either "over" or "under".

     '_u_n_i_v_e_r_s_e_G_e_n_e_I_d_s(_r)' accessor for vector of gene identifiers.

     '_i_s_C_o_n_d_i_t_i_o_n_a_l(_r)' Returns 'TRUE' if the instance has its
          conditional flag set


_A_u_t_h_o_r(_s):

     S. Falcon and N. LeMeur

_S_e_e _A_l_s_o:

     'HyperGResult-class' 'CoHyperGResult-class' 'hyperGTest'

