hyperGTest              package:GOstats              R Documentation

_H_y_p_e_r_g_e_o_m_e_t_r_i_c _T_e_s_t_s _f_o_r _G_O _t_e_r_m _a_s_s_o_c_i_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Given a 'GOHyperGParams' instance containing a set of unique
     Entrez Gene Identifiers, a microarray annotation data package
     name, and the GO ontology of interest, this function will compute
     Hypergeomtric p-values for over or under-representation of each GO
     term in the specified ontology among the GO annotations for the
     interesting genes.  The computations can be done conditionally
     based on the structure of the GO graph.

_A_r_g_u_m_e_n_t_s:

       p: A 'GOHyperGParams' instance 

_D_e_t_a_i_l_s:

     When 'conditional(p) == TRUE', the 'hyperGTest' function uses the
     structure of the GO graph to estimate for each term whether or not
     there is evidence beyond that which is provided by the term's
     children to call the term in question statistically
     overrepresented.

     The algorithm conditions on all child terms that are themselves
     significant at the specified p-value cutoff.  Given a subgraph of
     one of the three GO ontologies, the terms with no child categories
     are tested first.  Next the nodes whose children have already been
     tested are tested.  If any of a given node's children tested
     significant, the appropriate conditioning is performed.

_V_a_l_u_e:

     A 'GOHyperGResult' instance.

_A_u_t_h_o_r(_s):

     Seth Falcon

_R_e_f_e_r_e_n_c_e_s:

     FIXME

_S_e_e _A_l_s_o:

     'GOHyperGResult-class' 'geneCategoryHyperGeoTest'
     'geneGoHyperGeoTest' 'geneKeggHyperGeoTest'

