GOHyperGResult-class         package:GOstats         R Documentation

_C_l_a_s_s "_G_O_H_y_p_e_r_G_R_e_s_u_l_t"

_D_e_s_c_r_i_p_t_i_o_n:

     This class represents the results of a test for overrepresentation
     of GO categories among genes in a selected gene set based upon the
     Hypergeometric distribution.

     For details on extracting information from this object, be sure to
     read the accessor documentation in the Category package:
     HyperGResult-accessors.

_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("GOHyperGResult",
     ...)'.

_S_l_o_t_s:

     '_g_o_D_a_g': Object of class '"graph"' representing the DAG of GO
          terms tested.

     '_p_v_a_l_u_e._o_r_d_e_r': Object of class '"integer"'. The sort order of the
          computed p-values.

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"'.  The name of the
          annotation data package used in the analysis.

     '_g_e_n_e_I_d_s': Object of class '"ANY"'.  The intersection of the gene
          identifiers given as input and the computed gene universe.

     '_t_e_s_t_N_a_m_e': Object of class '"character"'. Identifies the testing
          method used to produce this result instance.

     '_p_v_a_l_u_e_C_u_t_o_f_f': Object of class '"numeric"'. The cutoff for
          significance used for some testing methods. Also used for
          pretty display in the 'show' method.

_E_x_t_e_n_d_s:

     Class '"HyperGResultBase"', directly.

_M_e_t_h_o_d_s:

     _g_o_D_a_g 'signature(r = "GOHyperGResult")': return the 'graph'
          instance representing the DAG of the GO terms that were
          tested.

     _c_o_n_d_G_e_n_e_I_d_U_n_i_v_e_r_s_e 'signature(r = "GOHyperGResult")': return a
          list named by the tested GO terms.  Each element of the list
          is a vector of the remaining gene identifiers (from the gene
          universe) annotated at the corresponding GO term after the
          identifiers from significant children were removed.  This is
          only available when the calculation performed used the
          conditional Hypergeometric algorithm.

     _s_u_m_m_a_r_y 'signature(r = "GOHyperGResult")': Returns a 'data.frame'
          summarizing the test result.  Optional arguments 'pvalue' and
          'categorySize' allow specification of maximum p-value and
          minimum cateogyrSize, respectively.  Optional argument
          'htmlLinks' is a logical value indicating whether to add HTML
          links (useful in conjunction with xtables print method with
          'type' set to '"html"').

     _h_t_m_l_R_e_p_o_r_t 'signature(r = "GOHyperGResult")': Write an HTML
          version of the table produced by the 'summary' method. The
          path of a file to write the report to can be specified using
          the 'file' argument.  The default is 'file=""' which will
          cause the report to be printed to the screen.  If you wish to
          create a single report comprising multiple results you can
          set 'append=TRUE'.  The default is 'FALSE' (overwrite
          preexisting report file).  You can specify a string to use as
          an identifier for each table by providing a value for the
          'label' argument.  Additional named arguments will be passed
          to the 'summary' method.

     _d_e_s_c_r_i_p_t_i_o_n 'signature(object = "GOHyperGResult")': Return a
          string giving a one-line description of the result.

_A_u_t_h_o_r(_s):

     Seth Falcon

_S_e_e _A_l_s_o:

     'GeneCategoryHyperGeoTestResult'

